Correlation between copy number variations of arm-level result and selected clinical features
Esophageal Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1SX6C61
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1SX6C61
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 82 arm-level events and 10 clinical features across 173 patients, no significant finding detected with Q value < 0.25.

  • No arm-level cnvs related to clinical features.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER NUMBER
PACK
YEARS
SMOKED 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
1p gain 33 (19%) 140 0.227
(0.876) 		0.155
(0.796) 		0.3
(0.891) 		0.638
(1.00) 		0.876
(1.00) 		0.65
(1.00) 		0.576
(1) 		0.857
(1.00) 		0.424
(0.961) 		0.563
(0.996)
1q gain 57 (33%) 116 0.107
(0.732) 		0.275
(0.876) 		0.881
(1.00) 		0.469
(0.978) 		0.722
(1.00) 		0.273
(0.876) 		0.0997
(0.714) 		0.43
(0.961) 		0.383
(0.939) 		1
(1.00)
2p gain 56 (32%) 117 0.513
(0.984) 		0.0433
(0.643) 		0.425
(0.961) 		0.22
(0.862) 		0.946
(1.00) 		0.695
(1.00) 		0.817
(1.00) 		0.138
(0.767) 		0.0198
(0.558) 		1
(1.00)
2q gain 42 (24%) 131 0.938
(1.00) 		0.176
(0.796) 		0.604
(1.00) 		0.267
(0.876) 		0.77
(1.00) 		1
(1.00) 		0.447
(0.964) 		0.685
(1.00) 		0.327
(0.903) 		1
(1.00)
3p gain 28 (16%) 145 0.483
(0.981) 		0.429
(0.961) 		0.203
(0.82) 		0.537
(0.996) 		0.125
(0.759) 		0.115
(0.741) 		0.77
(1.00) 		0.592
(1.00) 		0.515
(0.984) 		0.374
(0.939)
3q gain 70 (40%) 103 0.955
(1.00) 		0.00389
(0.4) 		0.899
(1.00) 		0.283
(0.876) 		0.676
(1.00) 		0.485
(0.981) 		0.825
(1.00) 		0.254
(0.876) 		0.492
(0.984) 		1
(1.00)
4p gain 16 (9%) 157 0.163
(0.796) 		0.787
(1.00) 		0.895
(1.00) 		0.906
(1.00) 		0.876
(1.00) 		0.511
(0.984) 		0.702
(1.00) 		0.575
(1) 		0.644
(1.00) 		0.32
(0.902)
4q gain 16 (9%) 157 0.163
(0.796) 		0.391
(0.939) 		0.986
(1.00) 		0.653
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.702
(1.00) 		0.621
(1.00) 		0.255
(0.876) 		1
(1.00)
5p gain 68 (39%) 105 0.183
(0.796) 		0.723
(1.00) 		0.265
(0.876) 		0.161
(0.796) 		0.26
(0.876) 		0.314
(0.894) 		0.12
(0.749) 		0.997
(1.00) 		0.797
(1.00) 		0.284
(0.876)
5q gain 19 (11%) 154 0.28
(0.876) 		0.28
(0.876) 		0.182
(0.796) 		0.6
(1.00) 		0.00263
(0.4) 		0.579
(1.00) 		0.307
(0.894) 		0.365
(0.939) 		0.246
(0.876) 		1
(1.00)
6p gain 36 (21%) 137 0.719
(1.00) 		0.283
(0.876) 		0.533
(0.995) 		0.851
(1.00) 		1
(1.00) 		0.11
(0.735) 		0.788
(1.00) 		0.836
(1.00) 		0.775
(1.00) 		1
(1.00)
6q gain 31 (18%) 142 0.813
(1.00) 		0.192
(0.803) 		0.123
(0.759) 		0.427
(0.961) 		0.831
(1.00) 		0.0134
(0.558) 		0.257
(0.876) 		0.586
(1.00) 		0.744
(1.00) 		1
(1.00)
7p gain 104 (60%) 69 0.78
(1.00) 		0.418
(0.961) 		0.636
(1.00) 		0.0395
(0.625) 		0.32
(0.902) 		0.184
(0.796) 		0.177
(0.796) 		0.248
(0.876) 		0.683
(1.00) 		0.293
(0.889)
7q gain 84 (49%) 89 0.63
(1.00) 		0.81
(1.00) 		0.624
(1.00) 		0.0174
(0.558) 		0.439
(0.964) 		0.178
(0.796) 		0.0485
(0.643) 		0.81
(1.00) 		0.598
(1.00) 		0.241
(0.876)
8p gain 65 (38%) 108 0.0822
(0.689) 		0.957
(1.00) 		0.708
(1.00) 		0.0831
(0.689) 		0.182
(0.796) 		0.723
(1.00) 		0.656
(1.00) 		0.188
(0.802) 		1
(1.00) 		1
(1.00)
8q gain 94 (54%) 79 0.262
(0.876) 		0.745
(1.00) 		0.137
(0.767) 		0.0138
(0.558) 		0.043
(0.643) 		0.732
(1.00) 		0.665
(1.00) 		0.787
(1.00) 		0.685
(1.00) 		0.587
(1.00)
9p gain 13 (8%) 160 0.345
(0.922) 		0.563
(0.996) 		0.939
(1.00) 		0.398
(0.939) 		0.104
(0.724) 		1
(1.00) 		1
(1.00) 		0.159
(0.796) 		0.284
(0.876) 		1
(1.00)
9q gain 29 (17%) 144 0.414
(0.961) 		0.363
(0.939) 		0.894
(1.00) 		0.326
(0.903) 		0.867
(1.00) 		1
(1.00) 		0.0837
(0.689) 		0.0601
(0.667) 		0.0152
(0.558) 		1
(1.00)
10p gain 38 (22%) 135 0.449
(0.964) 		0.956
(1.00) 		0.0465
(0.643) 		0.0548
(0.661) 		0.191
(0.803) 		0.0885
(0.689) 		0.295
(0.889) 		0.437
(0.964) 		0.696
(1.00) 		1
(1.00)
10q gain 29 (17%) 144 0.916
(1.00) 		0.942
(1.00) 		0.0444
(0.643) 		0.0592
(0.667) 		0.333
(0.903) 		0.13
(0.759) 		0.376
(0.939) 		0.0723
(0.689) 		0.359
(0.936) 		1
(1.00)
11p gain 38 (22%) 135 0.276
(0.876) 		0.391
(0.939) 		0.954
(1.00) 		0.263
(0.876) 		0.349
(0.925) 		0.393
(0.939) 		0.791
(1.00) 		0.101
(0.714) 		0.51
(0.984) 		1
(1.00)
11q gain 29 (17%) 144 0.932
(1.00) 		0.0459
(0.643) 		0.729
(1.00) 		0.219
(0.862) 		0.112
(0.735) 		1
(1.00) 		1
(1.00) 		0.465
(0.978) 		1
(1.00) 		1
(1.00)
12p gain 53 (31%) 120 0.359
(0.936) 		0.137
(0.767) 		0.14
(0.767) 		0.0827
(0.689) 		0.886
(1.00) 		0.0227
(0.558) 		0.0541
(0.661) 		0.166
(0.796) 		0.00882
(0.556) 		1
(1.00)
12q gain 36 (21%) 137 0.568
(1) 		0.299
(0.891) 		0.0251
(0.558) 		0.344
(0.922) 		0.572
(1) 		0.0188
(0.558) 		0.172
(0.796) 		0.016
(0.558) 		0.0881
(0.689) 		0.563
(0.996)
13q gain 40 (23%) 133 0.45
(0.964) 		0.8
(1.00) 		0.139
(0.767) 		0.0297
(0.558) 		0.309
(0.894) 		0.199
(0.817) 		1
(1.00) 		0.0764
(0.689) 		0.113
(0.735) 		0.0915
(0.701)
14q gain 44 (25%) 129 0.737
(1.00) 		0.299
(0.891) 		0.985
(1.00) 		0.0179
(0.558) 		0.369
(0.939) 		0.446
(0.964) 		0.00983
(0.558) 		1
(1.00) 		0.0381
(0.625) 		0.547
(0.996)
15q gain 27 (16%) 146 0.56
(0.996) 		0.595
(1.00) 		0.47
(0.978) 		0.785
(1.00) 		1
(1.00) 		0.359
(0.936) 		0.377
(0.939) 		0.0351
(0.607) 		1
(1.00) 		1
(1.00)
16p gain 37 (21%) 136 0.539
(0.996) 		0.931
(1.00) 		0.176
(0.796) 		0.13
(0.759) 		0.436
(0.964) 		0.416
(0.961) 		0.00264
(0.4) 		0.912
(1.00) 		0.0109
(0.558) 		0.558
(0.996)
16q gain 35 (20%) 138 0.0738
(0.689) 		0.901
(1.00) 		0.126
(0.759) 		0.128
(0.759) 		0.472
(0.978) 		0.0885
(0.689) 		0.0511
(0.645) 		0.867
(1.00) 		0.022
(0.558) 		1
(1.00)
17p gain 30 (17%) 143 0.855
(1.00) 		0.237
(0.876) 		0.895
(1.00) 		0.71
(1.00) 		0.328
(0.903) 		1
(1.00) 		0.259
(0.876) 		0.661
(1.00) 		0.403
(0.946) 		1
(1.00)
17q gain 41 (24%) 132 0.641
(1.00) 		0.728
(1.00) 		0.892
(1.00) 		0.848
(1.00) 		0.368
(0.939) 		1
(1.00) 		0.203
(0.82) 		0.186
(0.797) 		0.105
(0.724) 		1
(1.00)
18p gain 49 (28%) 124 0.281
(0.876) 		0.495
(0.984) 		0.471
(0.978) 		0.969
(1.00) 		0.649
(1.00) 		0.281
(0.876) 		0.0864
(0.689) 		0.745
(1.00) 		0.254
(0.876) 		1
(1.00)
18q gain 26 (15%) 147 0.312
(0.894) 		0.927
(1.00) 		0.12
(0.749) 		0.748
(1.00) 		0.483
(0.981) 		1
(1.00) 		1
(1.00) 		0.621
(1.00) 		1
(1.00) 		1
(1.00)
19p gain 26 (15%) 147 0.875
(1.00) 		0.755
(1.00) 		0.934
(1.00) 		0.936
(1.00) 		0.0479
(0.643) 		1
(1.00) 		0.0273
(0.558) 		0.753
(1.00) 		0.368
(0.939) 		0.426
(0.961)
19q gain 37 (21%) 136 0.876
(1.00) 		0.423
(0.961) 		0.558
(0.996) 		1
(1.00) 		0.42
(0.961) 		0.661
(1.00) 		0.0298
(0.558) 		0.812
(1.00) 		0.238
(0.876) 		0.497
(0.984)
20p gain 102 (59%) 71 0.0669
(0.689) 		0.383
(0.939) 		0.726
(1.00) 		0.464
(0.978) 		0.473
(0.978) 		0.298
(0.891) 		0.376
(0.939) 		0.829
(1.00) 		0.156
(0.796) 		0.252
(0.876)
20q gain 110 (64%) 63 0.13
(0.759) 		0.396
(0.939) 		0.899
(1.00) 		0.018
(0.558) 		0.198
(0.817) 		0.309
(0.894) 		0.171
(0.796) 		0.571
(1) 		0.0795
(0.689) 		0.269
(0.876)
21q gain 16 (9%) 157 0.231
(0.876) 		0.789
(1.00) 		0.669
(1.00) 		0.613
(1.00) 		0.487
(0.981) 		1
(1.00) 		0.702
(1.00) 		0.732
(1.00) 		0.0843
(0.689) 		1
(1.00)
22q gain 29 (17%) 144 0.926
(1.00) 		0.0325
(0.579) 		0.624
(1.00) 		0.246
(0.876) 		0.0135
(0.558) 		0.661
(1.00) 		0.77
(1.00) 		0.824
(1.00) 		0.00297
(0.4) 		0.563
(0.996)
xp gain 21 (12%) 152 0.874
(1.00) 		0.909
(1.00) 		0.553
(0.996) 		0.754
(1.00) 		0.0497
(0.643) 		1
(1.00) 		0.315
(0.894) 		0.283
(0.876) 		0.0258
(0.558) 		1
(1.00)
xq gain 35 (20%) 138 0.693
(1.00) 		0.475
(0.978) 		0.667
(1.00) 		0.501
(0.984) 		0.165
(0.796) 		0.687
(1.00) 		0.171
(0.796) 		0.972
(1.00) 		0.0363
(0.607) 		1
(1.00)
1p loss 34 (20%) 139 0.724
(1.00) 		0.523
(0.984) 		0.198
(0.817) 		1
(1.00) 		0.521
(0.984) 		0.163
(0.796) 		1
(1.00) 		0.607
(1.00) 		0.173
(0.796) 		1
(1.00)
1q loss 20 (12%) 153 0.0108
(0.558) 		0.284
(0.876) 		0.102
(0.714) 		0.332
(0.903) 		0.204
(0.82) 		0.112
(0.735) 		1
(1.00) 		0.432
(0.963) 		0.39
(0.939) 		1
(1.00)
2p loss 11 (6%) 162 0.0317
(0.578) 		0.195
(0.814) 		0.472
(0.978) 		0.273
(0.876) 		1
(1.00) 		1
(1.00) 		0.652
(1.00) 		0.95
(1.00) 		0.765
(1.00) 		1
(1.00)
2q loss 18 (10%) 155 0.539
(0.996) 		0.364
(0.939) 		0.915
(1.00) 		0.418
(0.961) 		0.613
(1.00) 		0.602
(1.00) 		0.719
(1.00) 		0.503
(0.984) 		1
(1.00) 		1
(1.00)
3p loss 86 (50%) 87 0.255
(0.876) 		0.0461
(0.643) 		0.307
(0.894) 		0.84
(1.00) 		0.158
(0.796) 		0.51
(0.984) 		0.388
(0.939) 		0.772
(1.00) 		0.00182
(0.4) 		0.0573
(0.661)
3q loss 32 (18%) 141 0.713
(1.00) 		0.778
(1.00) 		0.383
(0.939) 		0.748
(1.00) 		0.711
(1.00) 		1
(1.00) 		0.575
(1) 		0.676
(1.00) 		0.241
(0.876) 		1
(1.00)
4p loss 99 (57%) 74 0.0493
(0.643) 		0.256
(0.876) 		0.642
(1.00) 		0.0891
(0.689) 		0.332
(0.903) 		1
(1.00) 		0.508
(0.984) 		0.143
(0.767) 		0.0298
(0.558) 		0.558
(0.996)
4q loss 85 (49%) 88 0.0355
(0.607) 		0.0743
(0.689) 		0.346
(0.922) 		0.377
(0.939) 		0.612
(1.00) 		0.312
(0.894) 		0.273
(0.876) 		0.68
(1.00) 		0.168
(0.796) 		0.611
(1.00)
5p loss 45 (26%) 128 0.763
(1.00) 		0.272
(0.876) 		0.00597
(0.445) 		0.0272
(0.558) 		0.392
(0.939) 		0.686
(1.00) 		0.624
(1.00) 		0.834
(1.00) 		0.724
(1.00) 		0.153
(0.796)
5q loss 80 (46%) 93 0.355
(0.936) 		0.925
(1.00) 		0.131
(0.759) 		0.332
(0.903) 		0.209
(0.834) 		0.732
(1.00) 		0.665
(1.00) 		0.847
(1.00) 		0.556
(0.996) 		0.568
(1)
6p loss 36 (21%) 137 0.363
(0.939) 		0.313
(0.894) 		0.879
(1.00) 		0.19
(0.802) 		0.0828
(0.689) 		0.209
(0.834) 		1
(1.00) 		0.24
(0.876) 		0.256
(0.876) 		0.542
(0.996)
6q loss 37 (21%) 136 0.555
(0.996) 		0.501
(0.984) 		0.852
(1.00) 		0.305
(0.894) 		0.416
(0.961) 		1
(1.00) 		0.42
(0.961) 		0.278
(0.876) 		0.381
(0.939) 		0.542
(0.996)
7p loss 13 (8%) 160 0.517
(0.984) 		0.78
(1.00) 		0.909
(1.00) 		0.413
(0.961) 		0.711
(1.00) 		1
(1.00) 		0.395
(0.939) 		0.03
(0.558) 		0.774
(1.00) 		1
(1.00)
7q loss 22 (13%) 151 0.687
(1.00) 		0.306
(0.894) 		0.516
(0.984) 		0.00739
(0.505) 		0.256
(0.876) 		0.355
(0.936) 		1
(1.00) 		0.485
(0.981) 		1
(1.00) 		1
(1.00)
8p loss 58 (34%) 115 0.931
(1.00) 		0.873
(1.00) 		0.394
(0.939) 		0.668
(1.00) 		0.101
(0.714) 		1
(1.00) 		0.816
(1.00) 		0.0945
(0.713) 		0.444
(0.964) 		1
(1.00)
8q loss 22 (13%) 151 0.089
(0.689) 		0.602
(1.00) 		0.168
(0.796) 		0.491
(0.984) 		0.685
(1.00) 		0.614
(1.00) 		1
(1.00) 		0.701
(1.00) 		0.131
(0.759) 		1
(1.00)
9p loss 96 (55%) 77 0.507
(0.984) 		0.46
(0.978) 		0.499
(0.984) 		0.516
(0.984) 		0.177
(0.796) 		1
(1.00) 		0.0259
(0.558) 		0.76
(1.00) 		0.0551
(0.661) 		0.549
(0.996)
9q loss 61 (35%) 112 0.798
(1.00) 		0.393
(0.939) 		0.061
(0.667) 		0.444
(0.964) 		0.944
(1.00) 		0.273
(0.876) 		0.358
(0.936) 		0.143
(0.767) 		0.381
(0.939) 		0.0885
(0.689)
10p loss 44 (25%) 129 0.486
(0.981) 		0.722
(1.00) 		0.584
(1.00) 		0.0625
(0.674) 		0.0188
(0.558) 		0.45
(0.964) 		0.325
(0.903) 		0.78
(1.00) 		0.0556
(0.661) 		0.563
(0.996)
10q loss 43 (25%) 130 0.855
(1.00) 		0.388
(0.939) 		0.575
(1) 		0.085
(0.689) 		0.868
(1.00) 		1
(1.00) 		1
(1.00) 		0.521
(0.984) 		0.00107
(0.4) 		0.549
(0.996)
11p loss 47 (27%) 126 0.522
(0.984) 		0.507
(0.984) 		0.156
(0.796) 		0.71
(1.00) 		0.151
(0.796) 		0.453
(0.966) 		0.322
(0.902) 		0.807
(1.00) 		0.622
(1.00) 		1
(1.00)
11q loss 52 (30%) 121 0.182
(0.796) 		0.447
(0.964) 		0.184
(0.796) 		0.883
(1.00) 		0.0502
(0.643) 		0.711
(1.00) 		0.639
(1.00) 		0.648
(1.00) 		0.533
(0.995) 		1
(1.00)
12p loss 32 (18%) 141 0.439
(0.964) 		0.52
(0.984) 		0.595
(1.00) 		0.658
(1.00) 		0.468
(0.978) 		1
(1.00) 		0.398
(0.939) 		0.12
(0.749) 		0.0673
(0.689) 		1
(1.00)
12q loss 28 (16%) 145 0.69
(1.00) 		0.43
(0.961) 		0.044
(0.643) 		0.133
(0.762) 		0.562
(0.996) 		0.622
(1.00) 		0.0754
(0.689) 		0.0212
(0.558) 		0.00439
(0.4) 		1
(1.00)
13q loss 62 (36%) 111 0.252
(0.876) 		0.11
(0.735) 		0.687
(1.00) 		0.695
(1.00) 		0.735
(1.00) 		0.482
(0.981) 		0.0396
(0.625) 		1
(1.00) 		0.00437
(0.4) 		1
(1.00)
14q loss 43 (25%) 130 0.999
(1.00) 		0.295
(0.889) 		0.169
(0.796) 		0.335
(0.903) 		0.413
(0.961) 		0.688
(1.00) 		0.615
(1.00) 		0.619
(1.00) 		0.262
(0.876) 		0.45
(0.964)
15q loss 51 (29%) 122 0.454
(0.966) 		0.322
(0.902) 		0.667
(1.00) 		0.24
(0.876) 		0.614
(1.00) 		0.143
(0.767) 		0.81
(1.00) 		0.696
(1.00) 		0.529
(0.992) 		0.558
(0.996)
16p loss 53 (31%) 120 0.589
(1.00) 		0.688
(1.00) 		0.676
(1.00) 		0.291
(0.889) 		0.219
(0.862) 		1
(1.00) 		1
(1.00) 		0.831
(1.00) 		0.272
(0.876) 		0.0212
(0.558)
16q loss 50 (29%) 123 0.957
(1.00) 		0.467
(0.978) 		0.778
(1.00) 		0.397
(0.939) 		0.468
(0.978) 		1
(1.00) 		0.631
(1.00) 		0.718
(1.00) 		0.183
(0.796) 		0.0162
(0.558)
17p loss 68 (39%) 105 0.719
(1.00) 		0.0604
(0.667) 		0.478
(0.979) 		0.19
(0.802) 		0.498
(0.984) 		1
(1.00) 		1
(1.00) 		0.61
(1.00) 		0.076
(0.689) 		0.273
(0.876)
17q loss 24 (14%) 149 0.121
(0.749) 		0.893
(1.00) 		0.81
(1.00) 		0.584
(1.00) 		0.616
(1.00) 		1
(1.00) 		1
(1.00) 		0.991
(1.00) 		0.833
(1.00) 		0.0707
(0.689)
18p loss 67 (39%) 106 0.68
(1.00) 		0.1
(0.714) 		0.856
(1.00) 		0.0734
(0.689) 		0.268
(0.876) 		0.721
(1.00) 		0.501
(0.984) 		0.134
(0.762) 		0.111
(0.735) 		0.289
(0.888)
18q loss 95 (55%) 78 0.804
(1.00) 		0.259
(0.876) 		0.738
(1.00) 		0.495
(0.984) 		0.261
(0.876) 		0.507
(0.984) 		1
(1.00) 		0.248
(0.876) 		0.857
(1.00) 		1
(1.00)
19p loss 61 (35%) 112 0.811
(1.00) 		0.521
(0.984) 		0.762
(1.00) 		0.182
(0.796) 		0.089
(0.689) 		0.729
(1.00) 		0.646
(1.00) 		0.0564
(0.661) 		0.1
(0.714) 		0.547
(0.996)
19q loss 48 (28%) 125 0.677
(1.00) 		0.175
(0.796) 		0.982
(1.00) 		0.236
(0.876) 		0.339
(0.912) 		0.717
(1.00) 		1
(1.00) 		0.0956
(0.713) 		0.027
(0.558) 		0.558
(0.996)
20p loss 18 (10%) 155 0.0209
(0.558) 		0.895
(1.00) 		0.906
(1.00) 		0.577
(1) 		1
(1.00) 		0.597
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.312
(0.894) 		1
(1.00)
20q loss 8 (5%) 165 0.371
(0.939) 		0.742
(1.00) 		0.635
(1.00) 		0.0659
(0.689) 		0.282
(0.876) 		1
(1.00) 		1
(1.00) 		0.604
(1.00) 		0.442
(0.964) 		1
(1.00)
21q loss 99 (57%) 74 0.15
(0.796) 		0.268
(0.876) 		0.308
(0.894) 		0.761
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.378
(0.939) 		0.0954
(0.713) 		0.0683
(0.689) 		1
(1.00)
22q loss 70 (40%) 103 0.119
(0.749) 		0.327
(0.903) 		0.141
(0.767) 		0.0667
(0.689) 		0.13
(0.759) 		0.172
(0.796) 		1
(1.00) 		0.871
(1.00) 		0.476
(0.979) 		1
(1.00)
xp loss 57 (33%) 116 0.89
(1.00) 		0.656
(1.00) 		0.284
(0.876) 		0.335
(0.903) 		0.0886
(0.689) 		0.161
(0.796) 		0.0997
(0.714) 		0.00422
(0.4) 		0.0253
(0.558) 		1
(1.00)
xq loss 39 (23%) 134 0.93
(1.00) 		0.864
(1.00) 		0.736
(1.00) 		0.879
(1.00) 		0.423
(0.961) 		0.203
(0.82) 		0.294
(0.889) 		0.0051
(0.418) 		0.444
(0.964) 		0.563
(0.996)
Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ESCA-TP/15084413/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ESCA-TP/15078602/ESCA-TP.merged_data.txt

  • Number of patients = 173

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 10

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

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

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] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] 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)
[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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