Correlation between copy number variation genes (focal events) and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C19Z9396
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 copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C19Z9396
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 40 focal events and 8 molecular subtypes across 172 patients, 99 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 1q cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 2p cnv correlated to 'CN_CNMF'.

  • 2q cnv correlated to 'CN_CNMF'.

  • 3p cnv correlated to 'CN_CNMF'.

  • 3q cnv correlated to 'CN_CNMF'.

  • 4p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 4q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 5p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 5q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 6p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 6q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • 7p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 7q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 8q cnv correlated to 'METHLYATION_CNMF'.

  • 9p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 9q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 10p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 10q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • 11p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 11q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 12p cnv correlated to 'CN_CNMF'.

  • 12q cnv correlated to 'CN_CNMF'.

  • 13q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 14q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • 15q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16p cnv correlated to 'CN_CNMF'.

  • 16q cnv correlated to 'CN_CNMF'.

  • 17p cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 17q cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 18p cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • 18q cnv correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 19p cnv correlated to 'CN_CNMF'.

  • 19q cnv correlated to 'CN_CNMF'.

  • 22q cnv correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • xq cnv correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 40 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 99 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nCNV (%) 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
9q 26 (15%) 146 8.81e-07
(0.000249) 		1.32e-08
(4.02e-06) 		1.17e-08
(3.56e-06) 		1.09e-07
(3.24e-05) 		0.00475
(0.945) 		1.3e-05
(0.00346) 		0.0336
(1.00) 		1.83e-05
(0.00476)
10q 17 (10%) 155 6.87e-07
(0.000196) 		2.4e-07
(6.96e-05) 		0.000451
(0.106) 		0.0932
(1.00) 		0.605
(1.00) 		0.000372
(0.0889) 		0.507
(1.00) 		0.000635
(0.146)
14q 37 (22%) 135 2.82e-13
(8.87e-11) 		0.000432
(0.102) 		5.95e-05
(0.0151) 		4.08e-08
(1.22e-05) 		0.0941
(1.00) 		0.000843
(0.189) 		0.311
(1.00) 		0.0351
(1.00)
22q 42 (24%) 130 7.5e-07
(0.000214) 		1.18e-07
(3.48e-05) 		1.29e-07
(3.8e-05) 		0.000958
(0.213) 		0.0988
(1.00) 		1.61e-05
(0.00424) 		0.0294
(1.00) 		0.0182
(1.00)
1p 26 (15%) 146 1.74e-07
(5.11e-05) 		0.000735
(0.168) 		2.69e-05
(0.00697) 		0.000124
(0.0308) 		0.783
(1.00) 		0.677
(1.00) 		0.521
(1.00) 		0.87
(1.00)
4p 24 (14%) 148 2.9e-06
(8e-04) 		9.7e-09
(2.97e-06) 		3.28e-06
(0.000898) 		0.000532
(0.124) 		0.562
(1.00) 		0.0494
(1.00) 		0.456
(1.00) 		0.00325
(0.666)
7p 101 (59%) 71 1.14e-18
(3.66e-16) 		2.12e-07
(6.16e-05) 		1.43e-12
(4.48e-10) 		2.01e-07
(5.88e-05) 		0.0969
(1.00) 		0.00126
(0.277) 		0.17
(1.00) 		0.0408
(1.00)
7q 102 (59%) 70 4e-18
(1.28e-15) 		5.75e-07
(0.000166) 		2.02e-12
(6.29e-10) 		3.02e-07
(8.73e-05) 		0.149
(1.00) 		0.0054
(1.00) 		0.234
(1.00) 		0.126
(1.00)
9p 25 (15%) 147 7.59e-07
(0.000216) 		3.38e-08
(1.02e-05) 		3.66e-08
(1.1e-05) 		1.79e-05
(0.00469) 		0.00986
(1.00) 		0.00162
(0.35) 		0.045
(1.00) 		0.00197
(0.419)
10p 17 (10%) 155 1.51e-08
(4.56e-06) 		1.14e-06
(0.000318) 		0.000451
(0.106) 		0.26
(1.00) 		0.876
(1.00) 		0.00078
(0.176) 		0.842
(1.00) 		0.00123
(0.27)
17p 110 (64%) 62 1.05e-14
(3.32e-12) 		1.76e-05
(0.00462) 		9.26e-07
(0.000261) 		5.28e-06
(0.00142) 		0.0489
(1.00) 		0.00373
(0.754) 		0.101
(1.00) 		0.0854
(1.00)
1q 27 (16%) 145 1.38e-06
(0.000384) 		0.00394
(0.792) 		0.000341
(0.0822) 		0.000526
(0.123) 		0.603
(1.00) 		0.177
(1.00) 		0.523
(1.00) 		0.602
(1.00)
4q 24 (14%) 148 2.9e-06
(8e-04) 		2.21e-09
(6.79e-07) 		3.28e-06
(0.000898) 		0.00156
(0.338) 		0.843
(1.00) 		0.128
(1.00) 		0.355
(1.00) 		0.0125
(1.00)
5p 33 (19%) 139 7.13e-05
(0.018) 		3.5e-06
(0.000952) 		0.00594
(1.00) 		0.000122
(0.0306) 		0.0217
(1.00) 		0.122
(1.00) 		0.192
(1.00) 		0.163
(1.00)
5q 33 (19%) 139 0.000191
(0.0472) 		4.46e-05
(0.0114) 		0.00996
(1.00) 		0.000122
(0.0306) 		0.0217
(1.00) 		0.353
(1.00) 		0.192
(1.00) 		0.287
(1.00)
6p 20 (12%) 152 0.000544
(0.126) 		0.000899
(0.201) 		0.000357
(0.0858) 		0.0275
(1.00) 		0.0407
(1.00) 		0.123
(1.00) 		0.0911
(1.00) 		0.106
(1.00)
6q 21 (12%) 151 4.01e-06
(0.00109) 		3.3e-05
(0.00848) 		0.000423
(0.101) 		0.0121
(1.00) 		0.283
(1.00) 		0.173
(1.00) 		0.159
(1.00) 		0.152
(1.00)
11p 18 (10%) 154 2.72e-06
(0.000752) 		8.58e-06
(0.0023) 		0.0305
(1.00) 		0.000324
(0.0783) 		0.0229
(1.00) 		0.165
(1.00) 		0.518
(1.00) 		0.00927
(1.00)
11q 21 (12%) 151 3.45e-08
(1.04e-05) 		4.06e-08
(1.21e-05) 		0.011
(1.00) 		0.000532
(0.124) 		0.00966
(1.00) 		0.128
(1.00) 		0.417
(1.00) 		0.0334
(1.00)
13q 36 (21%) 136 5.57e-05
(0.0142) 		0.000199
(0.049) 		0.044
(1.00) 		0.000755
(0.171) 		0.0677
(1.00) 		0.0557
(1.00) 		0.123
(1.00) 		0.0675
(1.00)
15q 24 (14%) 148 5.82e-07
(0.000167) 		0.000618
(0.142) 		0.00291
(0.602) 		1.31e-06
(0.000366) 		0.302
(1.00) 		0.533
(1.00) 		0.354
(1.00) 		0.308
(1.00)
17q 117 (68%) 55 5.2e-12
(1.62e-09) 		0.00117
(0.259) 		9.37e-07
(0.000263) 		1.09e-05
(0.00291) 		0.293
(1.00) 		0.0743
(1.00) 		0.49
(1.00) 		0.122
(1.00)
18q 35 (20%) 137 0.00181
(0.386) 		7.14e-06
(0.00192) 		1.97e-05
(0.00513) 		0.000811
(0.182) 		0.0308
(1.00) 		0.0329
(1.00) 		0.186
(1.00) 		0.342
(1.00)
18p 37 (22%) 135 0.00142
(0.31) 		1.54e-05
(0.00409) 		3.04e-05
(0.00785) 		0.00212
(0.45) 		0.00974
(1.00) 		0.0299
(1.00) 		0.171
(1.00) 		0.189
(1.00)
2p 34 (20%) 138 1.27e-07
(3.76e-05) 		0.00446
(0.893) 		0.195
(1.00) 		0.665
(1.00) 		0.0771
(1.00) 		0.782
(1.00) 		0.0338
(1.00) 		0.857
(1.00)
2q 36 (21%) 136 7.07e-10
(2.18e-07) 		0.0187
(1.00) 		0.597
(1.00) 		0.455
(1.00) 		0.0859
(1.00) 		0.951
(1.00) 		0.0211
(1.00) 		0.863
(1.00)
3p 60 (35%) 112 7.81e-16
(2.48e-13) 		0.518
(1.00) 		0.352
(1.00) 		0.118
(1.00) 		0.839
(1.00) 		0.729
(1.00) 		0.809
(1.00) 		1
(1.00)
3q 59 (34%) 113 3.25e-17
(1.03e-14) 		0.223
(1.00) 		0.00179
(0.384) 		0.524
(1.00) 		0.348
(1.00) 		0.0266
(1.00) 		0.748
(1.00) 		0.124
(1.00)
8q 19 (11%) 153 0.00254
(0.533) 		0.000104
(0.026) 		0.0033
(0.672) 		0.0656
(1.00) 		0.00783
(1.00) 		0.0388
(1.00) 		0.0582
(1.00) 		0.0122
(1.00)
12p 69 (40%) 103 0.000301
(0.0731) 		0.605
(1.00) 		0.0287
(1.00) 		0.151
(1.00) 		0.389
(1.00) 		0.0801
(1.00) 		0.0806
(1.00) 		0.21
(1.00)
12q 68 (40%) 104 0.000236
(0.0575) 		0.461
(1.00) 		0.0156
(1.00) 		0.131
(1.00) 		0.288
(1.00) 		0.069
(1.00) 		0.0597
(1.00) 		0.209
(1.00)
16p 93 (54%) 79 1.68e-09
(5.17e-07) 		0.37
(1.00) 		0.00724
(1.00) 		0.00995
(1.00) 		0.0574
(1.00) 		0.0519
(1.00) 		0.0048
(0.951) 		0.0654
(1.00)
16q 90 (52%) 82 4.87e-10
(1.51e-07) 		0.349
(1.00) 		0.0024
(0.506) 		0.0227
(1.00) 		0.0274
(1.00) 		0.00617
(1.00) 		0.0058
(1.00) 		0.0346
(1.00)
19p 15 (9%) 157 0.000225
(0.0552) 		0.00306
(0.63) 		0.0297
(1.00) 		0.0114
(1.00) 		0.00737
(1.00) 		0.00343
(0.696) 		0.21
(1.00) 		0.00596
(1.00)
19q 14 (8%) 158 4.27e-05
(0.0109) 		0.00821
(1.00) 		0.029
(1.00) 		0.0491
(1.00) 		0.0127
(1.00) 		0.00811
(1.00) 		0.0737
(1.00) 		0.0178
(1.00)
xq 74 (43%) 98 1.18e-13
(3.72e-11) 		0.0521
(1.00) 		0.0611
(1.00) 		0.0732
(1.00) 		0.159
(1.00) 		0.222
(1.00) 		0.204
(1.00) 		0.668
(1.00)
8p 18 (10%) 154 0.138
(1.00) 		0.0188
(1.00) 		0.0903
(1.00) 		0.441
(1.00) 		0.0426
(1.00) 		0.0661
(1.00) 		0.107
(1.00) 		0.0215
(1.00)
20p 59 (34%) 113 0.00274
(0.572) 		0.109
(1.00) 		0.107
(1.00) 		0.42
(1.00) 		0.301
(1.00) 		0.69
(1.00) 		0.862
(1.00) 		0.778
(1.00)
20q 60 (35%) 112 0.00551
(1.00) 		0.109
(1.00) 		0.142
(1.00) 		0.452
(1.00) 		0.276
(1.00) 		0.729
(1.00) 		0.8
(1.00) 		0.747
(1.00)
21q 42 (24%) 130 0.00284
(0.591) 		0.0771
(1.00) 		0.0995
(1.00) 		0.0596
(1.00) 		0.312
(1.00) 		0.216
(1.00) 		0.0575
(1.00) 		0.823
(1.00)
'1p' versus 'CN_CNMF'

P value = 1.74e-07 (Fisher's exact test), Q value = 5.1e-05

Table S1.  Gene #1: '1p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
1P MUTATED 1 9 0 16
1P WILD-TYPE 32 59 37 18

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

'1p' versus 'METHLYATION_CNMF'

P value = 0.000735 (Fisher's exact test), Q value = 0.17

Table S2.  Gene #1: '1p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
1P MUTATED 5 15 5
1P WILD-TYPE 38 28 65

Figure S2.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'1p' versus 'MRNASEQ_CNMF'

P value = 2.69e-05 (Fisher's exact test), Q value = 0.007

Table S3.  Gene #1: '1p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
1P MUTATED 19 3 1 0
1P WILD-TYPE 39 46 30 23

Figure S3.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000124 (Fisher's exact test), Q value = 0.031

Table S4.  Gene #1: '1p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
1P MUTATED 12 8 3
1P WILD-TYPE 19 58 61

Figure S4.  Get High-res Image Gene #1: '1p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'1q' versus 'CN_CNMF'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.00038

Table S5.  Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
1Q MUTATED 1 9 1 16
1Q WILD-TYPE 32 59 36 18

Figure S5.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

'1q' versus 'MRNASEQ_CNMF'

P value = 0.000341 (Fisher's exact test), Q value = 0.082

Table S6.  Gene #2: '1q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
1Q MUTATED 18 3 3 0
1Q WILD-TYPE 40 46 28 23

Figure S6.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'1q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000526 (Fisher's exact test), Q value = 0.12

Table S7.  Gene #2: '1q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
1Q MUTATED 11 10 3
1Q WILD-TYPE 20 56 61

Figure S7.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'2p' versus 'CN_CNMF'

P value = 1.27e-07 (Fisher's exact test), Q value = 3.8e-05

Table S8.  Gene #3: '2p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
2P MUTATED 12 3 3 16
2P WILD-TYPE 21 65 34 18

Figure S8.  Get High-res Image Gene #3: '2p' versus Molecular Subtype #1: 'CN_CNMF'

'2q' versus 'CN_CNMF'

P value = 7.07e-10 (Fisher's exact test), Q value = 2.2e-07

Table S9.  Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
2Q MUTATED 13 2 3 18
2Q WILD-TYPE 20 66 34 16

Figure S9.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

'3p' versus 'CN_CNMF'

P value = 7.81e-16 (Fisher's exact test), Q value = 2.5e-13

Table S10.  Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
3P MUTATED 31 10 5 14
3P WILD-TYPE 2 58 32 20

Figure S10.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #1: 'CN_CNMF'

'3q' versus 'CN_CNMF'

P value = 3.25e-17 (Fisher's exact test), Q value = 1e-14

Table S11.  Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
3Q MUTATED 32 9 6 12
3Q WILD-TYPE 1 59 31 22

Figure S11.  Get High-res Image Gene #6: '3q' versus Molecular Subtype #1: 'CN_CNMF'

'4p' versus 'CN_CNMF'

P value = 2.9e-06 (Fisher's exact test), Q value = 8e-04

Table S12.  Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
4P MUTATED 1 7 1 15
4P WILD-TYPE 32 61 36 19

Figure S12.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

'4p' versus 'METHLYATION_CNMF'

P value = 9.7e-09 (Fisher's exact test), Q value = 3e-06

Table S13.  Gene #7: '4p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
4P MUTATED 1 18 2
4P WILD-TYPE 42 25 68

Figure S13.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4p' versus 'MRNASEQ_CNMF'

P value = 3.28e-06 (Fisher's exact test), Q value = 9e-04

Table S14.  Gene #7: '4p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
4P MUTATED 20 2 1 0
4P WILD-TYPE 38 47 30 23

Figure S14.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'4p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000532 (Fisher's exact test), Q value = 0.12

Table S15.  Gene #7: '4p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
4P MUTATED 11 9 3
4P WILD-TYPE 20 57 61

Figure S15.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4q' versus 'CN_CNMF'

P value = 2.9e-06 (Fisher's exact test), Q value = 8e-04

Table S16.  Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
4Q MUTATED 1 7 1 15
4Q WILD-TYPE 32 61 36 19

Figure S16.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

'4q' versus 'METHLYATION_CNMF'

P value = 2.21e-09 (Fisher's exact test), Q value = 6.8e-07

Table S17.  Gene #8: '4q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
4Q MUTATED 1 19 2
4Q WILD-TYPE 42 24 68

Figure S17.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'4q' versus 'MRNASEQ_CNMF'

P value = 3.28e-06 (Fisher's exact test), Q value = 9e-04

Table S18.  Gene #8: '4q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
4Q MUTATED 20 2 1 0
4Q WILD-TYPE 38 47 30 23

Figure S18.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'5p' versus 'CN_CNMF'

P value = 7.13e-05 (Fisher's exact test), Q value = 0.018

Table S19.  Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
5P MUTATED 3 14 1 15
5P WILD-TYPE 30 54 36 19

Figure S19.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #1: 'CN_CNMF'

'5p' versus 'METHLYATION_CNMF'

P value = 3.5e-06 (Fisher's exact test), Q value = 0.00095

Table S20.  Gene #9: '5p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
5P MUTATED 9 18 3
5P WILD-TYPE 34 25 67

Figure S20.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000122 (Fisher's exact test), Q value = 0.031

Table S21.  Gene #9: '5p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
5P MUTATED 10 19 3
5P WILD-TYPE 21 47 61

Figure S21.  Get High-res Image Gene #9: '5p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'5q' versus 'CN_CNMF'

P value = 0.000191 (Fisher's exact test), Q value = 0.047

Table S22.  Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
5Q MUTATED 3 15 1 14
5Q WILD-TYPE 30 53 36 20

Figure S22.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #1: 'CN_CNMF'

'5q' versus 'METHLYATION_CNMF'

P value = 4.46e-05 (Fisher's exact test), Q value = 0.011

Table S23.  Gene #10: '5q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
5Q MUTATED 9 17 4
5Q WILD-TYPE 34 26 66

Figure S23.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'5q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000122 (Fisher's exact test), Q value = 0.031

Table S24.  Gene #10: '5q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
5Q MUTATED 10 19 3
5Q WILD-TYPE 21 47 61

Figure S24.  Get High-res Image Gene #10: '5q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'6p' versus 'CN_CNMF'

P value = 0.000544 (Fisher's exact test), Q value = 0.13

Table S25.  Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
6P MUTATED 1 7 1 11
6P WILD-TYPE 32 61 36 23

Figure S25.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

'6p' versus 'METHLYATION_CNMF'

P value = 0.000899 (Fisher's exact test), Q value = 0.2

Table S26.  Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
6P MUTATED 2 12 4
6P WILD-TYPE 41 31 66

Figure S26.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6p' versus 'MRNASEQ_CNMF'

P value = 0.000357 (Fisher's exact test), Q value = 0.086

Table S27.  Gene #11: '6p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
6P MUTATED 15 4 0 0
6P WILD-TYPE 43 45 31 23

Figure S27.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'6q' versus 'CN_CNMF'

P value = 4.01e-06 (Fisher's exact test), Q value = 0.0011

Table S28.  Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
6Q MUTATED 1 5 1 14
6Q WILD-TYPE 32 63 36 20

Figure S28.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #1: 'CN_CNMF'

'6q' versus 'METHLYATION_CNMF'

P value = 3.3e-05 (Fisher's exact test), Q value = 0.0085

Table S29.  Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
6Q MUTATED 2 14 3
6Q WILD-TYPE 41 29 67

Figure S29.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'6q' versus 'MRNASEQ_CNMF'

P value = 0.000423 (Fisher's exact test), Q value = 0.1

Table S30.  Gene #12: '6q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
6Q MUTATED 16 3 1 0
6Q WILD-TYPE 42 46 30 23

Figure S30.  Get High-res Image Gene #12: '6q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p' versus 'CN_CNMF'

P value = 1.14e-18 (Fisher's exact test), Q value = 3.7e-16

Table S31.  Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
7P MUTATED 31 19 37 14
7P WILD-TYPE 2 49 0 20

Figure S31.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #1: 'CN_CNMF'

'7p' versus 'METHLYATION_CNMF'

P value = 2.12e-07 (Fisher's exact test), Q value = 6.2e-05

Table S32.  Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
7P MUTATED 20 14 57
7P WILD-TYPE 23 29 13

Figure S32.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7p' versus 'MRNASEQ_CNMF'

P value = 1.43e-12 (Fisher's exact test), Q value = 4.5e-10

Table S33.  Gene #13: '7p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
7P MUTATED 15 44 15 20
7P WILD-TYPE 43 5 16 3

Figure S33.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.01e-07 (Fisher's exact test), Q value = 5.9e-05

Table S34.  Gene #13: '7p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
7P MUTATED 9 32 53
7P WILD-TYPE 22 34 11

Figure S34.  Get High-res Image Gene #13: '7p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'7q' versus 'CN_CNMF'

P value = 4e-18 (Fisher's exact test), Q value = 1.3e-15

Table S35.  Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
7Q MUTATED 31 20 37 14
7Q WILD-TYPE 2 48 0 20

Figure S35.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #1: 'CN_CNMF'

'7q' versus 'METHLYATION_CNMF'

P value = 5.75e-07 (Fisher's exact test), Q value = 0.00017

Table S36.  Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
7Q MUTATED 20 15 57
7Q WILD-TYPE 23 28 13

Figure S36.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'7q' versus 'MRNASEQ_CNMF'

P value = 2.02e-12 (Fisher's exact test), Q value = 6.3e-10

Table S37.  Gene #14: '7q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
7Q MUTATED 15 44 16 20
7Q WILD-TYPE 43 5 15 3

Figure S37.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'7q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.02e-07 (Fisher's exact test), Q value = 8.7e-05

Table S38.  Gene #14: '7q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
7Q MUTATED 9 33 53
7Q WILD-TYPE 22 33 11

Figure S38.  Get High-res Image Gene #14: '7q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'8q' versus 'METHLYATION_CNMF'

P value = 0.000104 (Fisher's exact test), Q value = 0.026

Table S39.  Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
8Q MUTATED 2 12 2
8Q WILD-TYPE 41 31 68

Figure S39.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p' versus 'CN_CNMF'

P value = 7.59e-07 (Fisher's exact test), Q value = 0.00022

Table S40.  Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
9P MUTATED 1 9 0 15
9P WILD-TYPE 32 59 37 19

Figure S40.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #1: 'CN_CNMF'

'9p' versus 'METHLYATION_CNMF'

P value = 3.38e-08 (Fisher's exact test), Q value = 1e-05

Table S41.  Gene #17: '9p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
9P MUTATED 5 16 0
9P WILD-TYPE 38 27 70

Figure S41.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9p' versus 'MRNASEQ_CNMF'

P value = 3.66e-08 (Fisher's exact test), Q value = 1.1e-05

Table S42.  Gene #17: '9p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
9P MUTATED 22 0 1 1
9P WILD-TYPE 36 49 30 22

Figure S42.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.79e-05 (Fisher's exact test), Q value = 0.0047

Table S43.  Gene #17: '9p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
9P MUTATED 11 12 1
9P WILD-TYPE 20 54 63

Figure S43.  Get High-res Image Gene #17: '9p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q' versus 'CN_CNMF'

P value = 8.81e-07 (Fisher's exact test), Q value = 0.00025

Table S44.  Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
9Q MUTATED 1 10 0 15
9Q WILD-TYPE 32 58 37 19

Figure S44.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #1: 'CN_CNMF'

'9q' versus 'METHLYATION_CNMF'

P value = 1.32e-08 (Fisher's exact test), Q value = 4e-06

Table S45.  Gene #18: '9q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
9Q MUTATED 6 17 0
9Q WILD-TYPE 37 26 70

Figure S45.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'9q' versus 'MRNASEQ_CNMF'

P value = 1.17e-08 (Fisher's exact test), Q value = 3.6e-06

Table S46.  Gene #18: '9q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
9Q MUTATED 23 0 1 1
9Q WILD-TYPE 35 49 30 22

Figure S46.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'9q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-07 (Fisher's exact test), Q value = 3.2e-05

Table S47.  Gene #18: '9q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
9Q MUTATED 13 12 0
9Q WILD-TYPE 18 54 64

Figure S47.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.3e-05 (Fisher's exact test), Q value = 0.0035

Table S48.  Gene #18: '9q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
9Q MUTATED 6 2 18
9Q WILD-TYPE 12 78 56

Figure S48.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'9q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.83e-05 (Fisher's exact test), Q value = 0.0048

Table S49.  Gene #18: '9q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 87 71
9Q MUTATED 5 3 18
9Q WILD-TYPE 9 84 53

Figure S49.  Get High-res Image Gene #18: '9q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p' versus 'CN_CNMF'

P value = 1.51e-08 (Fisher's exact test), Q value = 4.6e-06

Table S50.  Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
10P MUTATED 1 1 1 14
10P WILD-TYPE 32 67 36 20

Figure S50.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #1: 'CN_CNMF'

'10p' versus 'METHLYATION_CNMF'

P value = 1.14e-06 (Fisher's exact test), Q value = 0.00032

Table S51.  Gene #19: '10p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
10P MUTATED 0 12 1
10P WILD-TYPE 43 31 69

Figure S51.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10p' versus 'MRNASEQ_CNMF'

P value = 0.000451 (Fisher's exact test), Q value = 0.11

Table S52.  Gene #19: '10p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
10P MUTATED 14 3 0 0
10P WILD-TYPE 44 46 31 23

Figure S52.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10p' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.18

Table S53.  Gene #19: '10p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
10P MUTATED 7 4 6
10P WILD-TYPE 11 76 68

Figure S53.  Get High-res Image Gene #19: '10p' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q' versus 'CN_CNMF'

P value = 6.87e-07 (Fisher's exact test), Q value = 2e-04

Table S54.  Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
10Q MUTATED 1 2 1 13
10Q WILD-TYPE 32 66 36 21

Figure S54.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #1: 'CN_CNMF'

'10q' versus 'METHLYATION_CNMF'

P value = 2.4e-07 (Fisher's exact test), Q value = 7e-05

Table S55.  Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
10Q MUTATED 0 13 1
10Q WILD-TYPE 43 30 69

Figure S55.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'10q' versus 'MRNASEQ_CNMF'

P value = 0.000451 (Fisher's exact test), Q value = 0.11

Table S56.  Gene #20: '10q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
10Q MUTATED 14 3 0 0
10Q WILD-TYPE 44 46 31 23

Figure S56.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'10q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000372 (Fisher's exact test), Q value = 0.089

Table S57.  Gene #20: '10q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
10Q MUTATED 7 3 7
10Q WILD-TYPE 11 77 67

Figure S57.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'10q' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000635 (Fisher's exact test), Q value = 0.15

Table S58.  Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 14 87 71
10Q MUTATED 6 4 7
10Q WILD-TYPE 8 83 64

Figure S58.  Get High-res Image Gene #20: '10q' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p' versus 'CN_CNMF'

P value = 2.72e-06 (Fisher's exact test), Q value = 0.00075

Table S59.  Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
11P MUTATED 0 6 0 12
11P WILD-TYPE 33 62 37 22

Figure S59.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #1: 'CN_CNMF'

'11p' versus 'METHLYATION_CNMF'

P value = 8.58e-06 (Fisher's exact test), Q value = 0.0023

Table S60.  Gene #21: '11p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
11P MUTATED 1 13 2
11P WILD-TYPE 42 30 68

Figure S60.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000324 (Fisher's exact test), Q value = 0.078

Table S61.  Gene #21: '11p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
11P MUTATED 9 7 1
11P WILD-TYPE 22 59 63

Figure S61.  Get High-res Image Gene #21: '11p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'11q' versus 'CN_CNMF'

P value = 3.45e-08 (Fisher's exact test), Q value = 1e-05

Table S62.  Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
11Q MUTATED 0 6 0 15
11Q WILD-TYPE 33 62 37 19

Figure S62.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #1: 'CN_CNMF'

'11q' versus 'METHLYATION_CNMF'

P value = 4.06e-08 (Fisher's exact test), Q value = 1.2e-05

Table S63.  Gene #22: '11q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
11Q MUTATED 1 17 2
11Q WILD-TYPE 42 26 68

Figure S63.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'11q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000532 (Fisher's exact test), Q value = 0.12

Table S64.  Gene #22: '11q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
11Q MUTATED 8 11 1
11Q WILD-TYPE 23 55 63

Figure S64.  Get High-res Image Gene #22: '11q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'12p' versus 'CN_CNMF'

P value = 0.000301 (Fisher's exact test), Q value = 0.073

Table S65.  Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
12P MUTATED 21 16 20 12
12P WILD-TYPE 12 52 17 22

Figure S65.  Get High-res Image Gene #23: '12p' versus Molecular Subtype #1: 'CN_CNMF'

'12q' versus 'CN_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.058

Table S66.  Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
12Q MUTATED 21 16 20 11
12Q WILD-TYPE 12 52 17 23

Figure S66.  Get High-res Image Gene #24: '12q' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'CN_CNMF'

P value = 5.57e-05 (Fisher's exact test), Q value = 0.014

Table S67.  Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
13Q MUTATED 7 10 2 17
13Q WILD-TYPE 26 58 35 17

Figure S67.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'METHLYATION_CNMF'

P value = 0.000199 (Fisher's exact test), Q value = 0.049

Table S68.  Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
13Q MUTATED 5 19 9
13Q WILD-TYPE 38 24 61

Figure S68.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'13q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000755 (Fisher's exact test), Q value = 0.17

Table S69.  Gene #25: '13q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
13Q MUTATED 15 13 8
13Q WILD-TYPE 16 53 56

Figure S69.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'CN_CNMF'

P value = 2.82e-13 (Fisher's exact test), Q value = 8.9e-11

Table S70.  Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
14Q MUTATED 1 12 0 24
14Q WILD-TYPE 32 56 37 10

Figure S70.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #1: 'CN_CNMF'

'14q' versus 'METHLYATION_CNMF'

P value = 0.000432 (Fisher's exact test), Q value = 0.1

Table S71.  Gene #26: '14q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
14Q MUTATED 10 17 6
14Q WILD-TYPE 33 26 64

Figure S71.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'14q' versus 'MRNASEQ_CNMF'

P value = 5.95e-05 (Fisher's exact test), Q value = 0.015

Table S72.  Gene #26: '14q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
14Q MUTATED 23 2 6 3
14Q WILD-TYPE 35 47 25 20

Figure S72.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4.08e-08 (Fisher's exact test), Q value = 1.2e-05

Table S73.  Gene #26: '14q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
14Q MUTATED 18 13 3
14Q WILD-TYPE 13 53 61

Figure S73.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'14q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000843 (Fisher's exact test), Q value = 0.19

Table S74.  Gene #26: '14q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
14Q MUTATED 9 9 19
14Q WILD-TYPE 9 71 55

Figure S74.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'15q' versus 'CN_CNMF'

P value = 5.82e-07 (Fisher's exact test), Q value = 0.00017

Table S75.  Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
15Q MUTATED 1 8 0 15
15Q WILD-TYPE 32 60 37 19

Figure S75.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #1: 'CN_CNMF'

'15q' versus 'METHLYATION_CNMF'

P value = 0.000618 (Fisher's exact test), Q value = 0.14

Table S76.  Gene #27: '15q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
15Q MUTATED 7 13 3
15Q WILD-TYPE 36 30 67

Figure S76.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'15q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.00037

Table S77.  Gene #27: '15q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
15Q MUTATED 13 7 1
15Q WILD-TYPE 18 59 63

Figure S77.  Get High-res Image Gene #27: '15q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p' versus 'CN_CNMF'

P value = 1.68e-09 (Fisher's exact test), Q value = 5.2e-07

Table S78.  Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
16P MUTATED 33 29 15 16
16P WILD-TYPE 0 39 22 18

Figure S78.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

'16q' versus 'CN_CNMF'

P value = 4.87e-10 (Fisher's exact test), Q value = 1.5e-07

Table S79.  Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
16Q MUTATED 33 29 14 14
16Q WILD-TYPE 0 39 23 20

Figure S79.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'CN_CNMF'

P value = 1.05e-14 (Fisher's exact test), Q value = 3.3e-12

Table S80.  Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
17P MUTATED 32 24 36 18
17P WILD-TYPE 1 44 1 16

Figure S80.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'17p' versus 'METHLYATION_CNMF'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.0046

Table S81.  Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
17P MUTATED 19 22 58
17P WILD-TYPE 24 21 12

Figure S81.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'17p' versus 'MRNASEQ_CNMF'

P value = 9.26e-07 (Fisher's exact test), Q value = 0.00026

Table S82.  Gene #30: '17p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
17P MUTATED 23 44 19 15
17P WILD-TYPE 35 5 12 8

Figure S82.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5.28e-06 (Fisher's exact test), Q value = 0.0014

Table S83.  Gene #30: '17p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
17P MUTATED 12 35 54
17P WILD-TYPE 19 31 10

Figure S83.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17q' versus 'CN_CNMF'

P value = 5.2e-12 (Fisher's exact test), Q value = 1.6e-09

Table S84.  Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
17Q MUTATED 32 29 36 20
17Q WILD-TYPE 1 39 1 14

Figure S84.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #1: 'CN_CNMF'

'17q' versus 'MRNASEQ_CNMF'

P value = 9.37e-07 (Fisher's exact test), Q value = 0.00026

Table S85.  Gene #31: '17q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
17Q MUTATED 25 45 22 16
17Q WILD-TYPE 33 4 9 7

Figure S85.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'17q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.09e-05 (Fisher's exact test), Q value = 0.0029

Table S86.  Gene #31: '17q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
17Q MUTATED 12 41 55
17Q WILD-TYPE 19 25 9

Figure S86.  Get High-res Image Gene #31: '17q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'18p' versus 'METHLYATION_CNMF'

P value = 1.54e-05 (Fisher's exact test), Q value = 0.0041

Table S87.  Gene #32: '18p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
18P MUTATED 4 20 8
18P WILD-TYPE 39 23 62

Figure S87.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18p' versus 'MRNASEQ_CNMF'

P value = 3.04e-05 (Fisher's exact test), Q value = 0.0078

Table S88.  Gene #32: '18p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
18P MUTATED 24 3 4 2
18P WILD-TYPE 34 46 27 21

Figure S88.  Get High-res Image Gene #32: '18p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q' versus 'METHLYATION_CNMF'

P value = 7.14e-06 (Fisher's exact test), Q value = 0.0019

Table S89.  Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
18Q MUTATED 4 20 7
18Q WILD-TYPE 39 23 63

Figure S89.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'18q' versus 'MRNASEQ_CNMF'

P value = 1.97e-05 (Fisher's exact test), Q value = 0.0051

Table S90.  Gene #33: '18q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
18Q MUTATED 23 2 4 2
18Q WILD-TYPE 35 47 27 21

Figure S90.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'18q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000811 (Fisher's exact test), Q value = 0.18

Table S91.  Gene #33: '18q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
18Q MUTATED 11 16 4
18Q WILD-TYPE 20 50 60

Figure S91.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'19p' versus 'CN_CNMF'

P value = 0.000225 (Fisher's exact test), Q value = 0.055

Table S92.  Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
19P MUTATED 1 2 2 10
19P WILD-TYPE 32 66 35 24

Figure S92.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #1: 'CN_CNMF'

'19q' versus 'CN_CNMF'

P value = 4.27e-05 (Fisher's exact test), Q value = 0.011

Table S93.  Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
19Q MUTATED 1 1 2 10
19Q WILD-TYPE 32 67 35 24

Figure S93.  Get High-res Image Gene #35: '19q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'CN_CNMF'

P value = 7.5e-07 (Fisher's exact test), Q value = 0.00021

Table S94.  Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
22Q MUTATED 1 16 5 20
22Q WILD-TYPE 32 52 32 14

Figure S94.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #1: 'CN_CNMF'

'22q' versus 'METHLYATION_CNMF'

P value = 1.18e-07 (Fisher's exact test), Q value = 3.5e-05

Table S95.  Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 43 70
22Q MUTATED 5 25 9
22Q WILD-TYPE 38 18 61

Figure S95.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'22q' versus 'MRNASEQ_CNMF'

P value = 1.29e-07 (Fisher's exact test), Q value = 3.8e-05

Table S96.  Gene #39: '22q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 58 49 31 23
22Q MUTATED 29 5 5 0
22Q WILD-TYPE 29 44 26 23

Figure S96.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'22q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000958 (Fisher's exact test), Q value = 0.21

Table S97.  Gene #39: '22q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 66 64
22Q MUTATED 11 22 6
22Q WILD-TYPE 20 44 58

Figure S97.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'22q' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.61e-05 (Fisher's exact test), Q value = 0.0042

Table S98.  Gene #39: '22q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 80 74
22Q MUTATED 13 13 16
22Q WILD-TYPE 5 67 58

Figure S98.  Get High-res Image Gene #39: '22q' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'xq' versus 'CN_CNMF'

P value = 1.18e-13 (Fisher's exact test), Q value = 3.7e-11

Table S99.  Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 33 68 37 34
XQ MUTATED 30 9 16 19
XQ WILD-TYPE 3 59 21 15

Figure S99.  Get High-res Image Gene #40: 'xq' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Molecular subtype file = KIRP-TP.transferedmergedcluster.txt

  • Number of patients = 172

  • Number of significantly focal cnvs = 40

  • Number of molecular subtypes = 8

  • Exclude genes that fewer than K tumors have alterations, 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)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle