Correlation between copy number variation genes (focal events) and molecular subtypes
Liver Hepatocellular Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1416VGJ
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/C1416VGJ
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 165 patients, 23 significant findings detected with P value < 0.05 and Q value < 0.25.

  • 1q cnv correlated to 'CN_CNMF'.

  • 2q cnv correlated to 'CN_CNMF'.

  • 3p cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 4p cnv correlated to 'CN_CNMF'.

  • 4q cnv correlated to 'CN_CNMF'.

  • 6p cnv correlated to 'CN_CNMF'.

  • 8p cnv correlated to 'CN_CNMF'.

  • 8q cnv correlated to 'CN_CNMF'.

  • 13q cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • 14q cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 16p cnv correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • 16q cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • 17p cnv correlated to 'CN_CNMF'.

  • 18q cnv correlated to 'CN_CNMF'.

  • 19p cnv correlated to 'METHLYATION_CNMF'.

  • 20p cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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, 23 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 Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
16p 60 (36%) 105 0.00041
(0.125) 		0.126
(1.00) 		1.06e-07
(3.36e-05) 		0.000149
(0.0462) 		0.608
(1.00) 		0.0184
(1.00) 		0.0049
(1.00) 		0.00812
(1.00)
3p 35 (21%) 130 0.0105
(1.00) 		0.0939
(1.00) 		0.000674
(0.202) 		0.00058
(0.174) 		0.914
(1.00) 		0.123
(1.00) 		0.126
(1.00) 		0.0362
(1.00)
13q 67 (41%) 98 0.000236
(0.0725) 		0.0336
(1.00) 		1.41e-05
(0.00442) 		0.00215
(0.62) 		0.3
(1.00) 		0.0681
(1.00) 		0.0583
(1.00) 		0.0496
(1.00)
14q 57 (35%) 108 0.0135
(1.00) 		0.225
(1.00) 		0.00018
(0.0555) 		0.000421
(0.128) 		0.246
(1.00) 		0.584
(1.00) 		0.287
(1.00) 		0.405
(1.00)
16q 66 (40%) 99 0.00137
(0.399) 		0.0298
(1.00) 		1.01e-06
(0.000318) 		0.000222
(0.0683) 		0.121
(1.00) 		0.112
(1.00) 		0.293
(1.00) 		0.157
(1.00)
20p 57 (35%) 108 0.000805
(0.241) 		0.00388
(1.00) 		0.00272
(0.772) 		0.000829
(0.247) 		0.929
(1.00) 		0.119
(1.00) 		0.188
(1.00) 		0.0976
(1.00)
1q 104 (63%) 61 2.43e-07
(7.67e-05) 		0.000905
(0.269) 		0.00369
(1.00) 		0.0525
(1.00) 		0.0266
(1.00) 		0.851
(1.00) 		0.249
(1.00) 		0.436
(1.00)
2q 35 (21%) 130 0.000249
(0.0761) 		0.791
(1.00) 		0.226
(1.00) 		0.607
(1.00) 		0.0211
(1.00) 		0.144
(1.00) 		0.565
(1.00) 		0.274
(1.00)
4p 49 (30%) 116 4.4e-05
(0.0137) 		0.0961
(1.00) 		0.000955
(0.282) 		0.0648
(1.00) 		0.668
(1.00) 		0.945
(1.00) 		0.343
(1.00) 		0.69
(1.00)
4q 58 (35%) 107 5.57e-08
(1.77e-05) 		0.0413
(1.00) 		0.00135
(0.394) 		0.395
(1.00) 		0.478
(1.00) 		1
(1.00) 		0.335
(1.00) 		0.815
(1.00)
6p 62 (38%) 103 8.87e-05
(0.0276) 		0.0314
(1.00) 		0.0159
(1.00) 		0.116
(1.00) 		0.338
(1.00) 		0.901
(1.00) 		0.36
(1.00) 		0.934
(1.00)
8p 111 (67%) 54 3.49e-08
(1.11e-05) 		0.0249
(1.00) 		0.00971
(1.00) 		0.0492
(1.00) 		0.0921
(1.00) 		0.102
(1.00) 		1
(1.00) 		0.157
(1.00)
8q 99 (60%) 66 1.37e-13
(4.37e-11) 		0.498
(1.00) 		0.0369
(1.00) 		0.02
(1.00) 		0.0848
(1.00) 		0.554
(1.00) 		1
(1.00) 		0.712
(1.00)
17p 100 (61%) 65 5.84e-06
(0.00183) 		0.859
(1.00) 		0.033
(1.00) 		0.0521
(1.00) 		0.0166
(1.00) 		0.00894
(1.00) 		0.403
(1.00) 		0.015
(1.00)
18q 45 (27%) 120 0.000514
(0.156) 		0.00986
(1.00) 		0.00443
(1.00) 		0.0127
(1.00) 		0.94
(1.00) 		0.185
(1.00) 		0.319
(1.00) 		0.109
(1.00)
19p 54 (33%) 111 0.000906
(0.269) 		0.000563
(0.17) 		0.0187
(1.00) 		0.0249
(1.00) 		0.79
(1.00) 		0.324
(1.00) 		0.134
(1.00) 		0.217
(1.00)
1p 63 (38%) 102 0.00314
(0.888) 		0.0278
(1.00) 		0.0134
(1.00) 		0.0154
(1.00) 		0.15
(1.00) 		0.882
(1.00) 		0.325
(1.00) 		0.952
(1.00)
2p 38 (23%) 127 0.00119
(0.349) 		0.968
(1.00) 		0.0674
(1.00) 		0.415
(1.00) 		0.0293
(1.00) 		0.295
(1.00) 		0.141
(1.00) 		0.519
(1.00)
3q 28 (17%) 137 0.107
(1.00) 		0.31
(1.00) 		0.0524
(1.00) 		0.036
(1.00) 		0.832
(1.00) 		0.399
(1.00) 		0.497
(1.00) 		0.356
(1.00)
5p 73 (44%) 92 0.00188
(0.543) 		0.0215
(1.00) 		0.395
(1.00) 		0.452
(1.00) 		0.799
(1.00) 		0.823
(1.00) 		0.559
(1.00) 		0.816
(1.00)
5q 62 (38%) 103 0.00118
(0.347) 		0.0122
(1.00) 		0.369
(1.00) 		0.447
(1.00) 		0.915
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.956
(1.00)
6q 75 (45%) 90 0.0183
(1.00) 		0.223
(1.00) 		0.0209
(1.00) 		0.0333
(1.00) 		0.754
(1.00) 		0.602
(1.00) 		0.493
(1.00) 		0.778
(1.00)
7p 60 (36%) 105 0.0297
(1.00) 		0.117
(1.00) 		0.046
(1.00) 		0.34
(1.00) 		0.114
(1.00) 		0.0758
(1.00) 		0.459
(1.00) 		0.447
(1.00)
7q 65 (39%) 100 0.27
(1.00) 		0.0588
(1.00) 		0.0532
(1.00) 		0.313
(1.00) 		0.166
(1.00) 		0.127
(1.00) 		0.424
(1.00) 		0.673
(1.00)
9p 59 (36%) 106 0.00641
(1.00) 		0.227
(1.00) 		0.0703
(1.00) 		0.0478
(1.00) 		0.344
(1.00) 		0.489
(1.00) 		0.884
(1.00) 		0.529
(1.00)
9q 59 (36%) 106 0.0872
(1.00) 		0.471
(1.00) 		0.00609
(1.00) 		0.00228
(0.651) 		0.751
(1.00) 		0.661
(1.00) 		0.662
(1.00) 		0.303
(1.00)
10p 45 (27%) 120 0.408
(1.00) 		0.259
(1.00) 		0.0861
(1.00) 		0.0412
(1.00) 		0.82
(1.00) 		0.701
(1.00) 		0.422
(1.00) 		0.594
(1.00)
10q 50 (30%) 115 0.369
(1.00) 		0.354
(1.00) 		0.0105
(1.00) 		0.0412
(1.00) 		0.927
(1.00) 		0.499
(1.00) 		0.768
(1.00) 		0.42
(1.00)
11p 40 (24%) 125 0.185
(1.00) 		0.484
(1.00) 		0.0509
(1.00) 		0.308
(1.00) 		0.544
(1.00) 		0.448
(1.00) 		0.226
(1.00) 		0.366
(1.00)
11q 44 (27%) 121 0.478
(1.00) 		0.462
(1.00) 		0.114
(1.00) 		0.466
(1.00) 		0.626
(1.00) 		0.859
(1.00) 		0.791
(1.00) 		0.807
(1.00)
12p 50 (30%) 115 0.0884
(1.00) 		0.519
(1.00) 		0.00322
(0.907) 		0.131
(1.00) 		0.211
(1.00) 		0.216
(1.00) 		0.754
(1.00) 		0.194
(1.00)
12q 40 (24%) 125 0.11
(1.00) 		0.67
(1.00) 		0.018
(1.00) 		0.105
(1.00) 		0.876
(1.00) 		0.186
(1.00) 		0.878
(1.00) 		0.184
(1.00)
15q 46 (28%) 119 0.00798
(1.00) 		0.348
(1.00) 		0.0586
(1.00) 		0.0283
(1.00) 		0.647
(1.00) 		0.857
(1.00) 		0.266
(1.00) 		0.834
(1.00)
17q 64 (39%) 101 0.0033
(0.928) 		0.345
(1.00) 		0.123
(1.00) 		0.232
(1.00) 		1
(1.00) 		0.635
(1.00) 		0.168
(1.00) 		0.734
(1.00)
18p 43 (26%) 122 0.00508
(1.00) 		0.0166
(1.00) 		0.0111
(1.00) 		0.0741
(1.00) 		0.965
(1.00) 		0.115
(1.00) 		0.388
(1.00) 		0.143
(1.00)
19q 52 (32%) 113 0.00227
(0.65) 		0.00358
(0.999) 		0.0105
(1.00) 		0.00453
(1.00) 		0.671
(1.00) 		0.278
(1.00) 		0.109
(1.00) 		0.189
(1.00)
20q 55 (33%) 110 0.00187
(0.542) 		0.0179
(1.00) 		0.00885
(1.00) 		0.00386
(1.00) 		0.91
(1.00) 		0.68
(1.00) 		0.221
(1.00) 		0.592
(1.00)
21q 60 (36%) 105 0.00347
(0.972) 		0.227
(1.00) 		0.01
(1.00) 		0.186
(1.00) 		0.00694
(1.00) 		0.0928
(1.00) 		0.371
(1.00) 		0.0543
(1.00)
22q 59 (36%) 106 0.0103
(1.00) 		0.0938
(1.00) 		0.00252
(0.717) 		0.00493
(1.00) 		0.957
(1.00) 		0.876
(1.00) 		0.385
(1.00) 		0.739
(1.00)
xq 54 (33%) 111 0.0105
(1.00) 		0.0289
(1.00) 		0.164
(1.00) 		0.0158
(1.00) 		0.23
(1.00) 		0.434
(1.00) 		0.126
(1.00) 		0.515
(1.00)
'1q' versus 'CN_CNMF'

P value = 2.43e-07 (Fisher's exact test), Q value = 7.7e-05

Table S1.  Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
1Q MUTATED 40 24 40
1Q WILD-TYPE 6 39 16

Figure S1.  Get High-res Image Gene #2: '1q' versus Molecular Subtype #1: 'CN_CNMF'

'2q' versus 'CN_CNMF'

P value = 0.000249 (Fisher's exact test), Q value = 0.076

Table S2.  Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
2Q MUTATED 11 4 20
2Q WILD-TYPE 35 59 36

Figure S2.  Get High-res Image Gene #4: '2q' versus Molecular Subtype #1: 'CN_CNMF'

'3p' versus 'MRNASEQ_CNMF'

P value = 0.000674 (Chi-square test), Q value = 0.2

Table S3.  Gene #5: '3p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 17 14 14 29 21 6 17 16 9
3P MUTATED 5 8 1 4 0 3 6 1 2
3P WILD-TYPE 12 6 13 25 21 3 11 15 7

Figure S3.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'3p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.17

Table S4.  Gene #5: '3p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 27 37 57
3P MUTATED 1 1 7 21
3P WILD-TYPE 21 26 30 36

Figure S4.  Get High-res Image Gene #5: '3p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'4p' versus 'CN_CNMF'

P value = 4.4e-05 (Fisher's exact test), Q value = 0.014

Table S5.  Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
4P MUTATED 13 8 28
4P WILD-TYPE 33 55 28

Figure S5.  Get High-res Image Gene #7: '4p' versus Molecular Subtype #1: 'CN_CNMF'

'4q' versus 'CN_CNMF'

P value = 5.57e-08 (Fisher's exact test), Q value = 1.8e-05

Table S6.  Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
4Q MUTATED 15 8 35
4Q WILD-TYPE 31 55 21

Figure S6.  Get High-res Image Gene #8: '4q' versus Molecular Subtype #1: 'CN_CNMF'

'6p' versus 'CN_CNMF'

P value = 8.87e-05 (Fisher's exact test), Q value = 0.028

Table S7.  Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
6P MUTATED 24 11 27
6P WILD-TYPE 22 52 29

Figure S7.  Get High-res Image Gene #11: '6p' versus Molecular Subtype #1: 'CN_CNMF'

'8p' versus 'CN_CNMF'

P value = 3.49e-08 (Fisher's exact test), Q value = 1.1e-05

Table S8.  Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
8P MUTATED 43 27 41
8P WILD-TYPE 3 36 15

Figure S8.  Get High-res Image Gene #15: '8p' versus Molecular Subtype #1: 'CN_CNMF'

'8q' versus 'CN_CNMF'

P value = 1.37e-13 (Fisher's exact test), Q value = 4.4e-11

Table S9.  Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
8Q MUTATED 45 19 35
8Q WILD-TYPE 1 44 21

Figure S9.  Get High-res Image Gene #16: '8q' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'CN_CNMF'

P value = 0.000236 (Fisher's exact test), Q value = 0.072

Table S10.  Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
13Q MUTATED 14 18 35
13Q WILD-TYPE 32 45 21

Figure S10.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #1: 'CN_CNMF'

'13q' versus 'MRNASEQ_CNMF'

P value = 1.41e-05 (Chi-square test), Q value = 0.0044

Table S11.  Gene #25: '13q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 17 14 14 29 21 6 17 16 9
13Q MUTATED 7 11 1 10 2 6 11 7 4
13Q WILD-TYPE 10 3 13 19 19 0 6 9 5

Figure S11.  Get High-res Image Gene #25: '13q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Chi-square test), Q value = 0.056

Table S12.  Gene #26: '14q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 17 14 14 29 21 6 17 16 9
14Q MUTATED 9 9 1 9 2 5 7 6 7
14Q WILD-TYPE 8 5 13 20 19 1 10 10 2

Figure S12.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'14q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000421 (Fisher's exact test), Q value = 0.13

Table S13.  Gene #26: '14q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 27 37 57
14Q MUTATED 3 6 13 33
14Q WILD-TYPE 19 21 24 24

Figure S13.  Get High-res Image Gene #26: '14q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16p' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.13

Table S14.  Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
16P MUTATED 13 15 32
16P WILD-TYPE 33 48 24

Figure S14.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #1: 'CN_CNMF'

'16p' versus 'MRNASEQ_CNMF'

P value = 1.06e-07 (Chi-square test), Q value = 3.4e-05

Table S15.  Gene #28: '16p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 17 14 14 29 21 6 17 16 9
16P MUTATED 7 8 1 7 2 4 17 5 3
16P WILD-TYPE 10 6 13 22 19 2 0 11 6

Figure S15.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000149 (Fisher's exact test), Q value = 0.046

Table S16.  Gene #28: '16p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 27 37 57
16P MUTATED 3 7 10 34
16P WILD-TYPE 19 20 27 23

Figure S16.  Get High-res Image Gene #28: '16p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'16q' versus 'MRNASEQ_CNMF'

P value = 1.01e-06 (Chi-square test), Q value = 0.00032

Table S17.  Gene #29: '16q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 17 14 14 29 21 6 17 16 9
16Q MUTATED 9 7 2 8 4 5 17 4 3
16Q WILD-TYPE 8 7 12 21 17 1 0 12 6

Figure S17.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'16q' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000222 (Fisher's exact test), Q value = 0.068

Table S18.  Gene #29: '16q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 27 37 57
16Q MUTATED 5 6 12 36
16Q WILD-TYPE 17 21 25 21

Figure S18.  Get High-res Image Gene #29: '16q' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'17p' versus 'CN_CNMF'

P value = 5.84e-06 (Fisher's exact test), Q value = 0.0018

Table S19.  Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
17P MUTATED 21 31 48
17P WILD-TYPE 25 32 8

Figure S19.  Get High-res Image Gene #30: '17p' versus Molecular Subtype #1: 'CN_CNMF'

'18q' versus 'CN_CNMF'

P value = 0.000514 (Fisher's exact test), Q value = 0.16

Table S20.  Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
18Q MUTATED 15 7 23
18Q WILD-TYPE 31 56 33

Figure S20.  Get High-res Image Gene #33: '18q' versus Molecular Subtype #1: 'CN_CNMF'

'19p' versus 'METHLYATION_CNMF'

P value = 0.000563 (Fisher's exact test), Q value = 0.17

Table S21.  Gene #34: '19p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 42 73
19P MUTATED 12 24 17
19P WILD-TYPE 37 18 56

Figure S21.  Get High-res Image Gene #34: '19p' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'20p' versus 'CN_CNMF'

P value = 0.000805 (Fisher's exact test), Q value = 0.24

Table S22.  Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 63 56
20P MUTATED 19 11 27
20P WILD-TYPE 27 52 29

Figure S22.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #1: 'CN_CNMF'

'20p' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000829 (Fisher's exact test), Q value = 0.25

Table S23.  Gene #36: '20p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 22 27 37 57
20P MUTATED 2 7 14 31
20P WILD-TYPE 20 20 23 26

Figure S23.  Get High-res Image Gene #36: '20p' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

Methods & Data
Input

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

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

  • Number of patients = 165

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

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

Download Results

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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