Correlation between copy number variations of arm-level result and selected clinical features
Rectum Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1NZ85Q4
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1NZ85Q4
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 75 arm-level results and 11 clinical features across 162 patients, 2 significant findings detected with Q value < 0.25.

  • 14q gain cnv correlated to 'LYMPH.NODE.METASTASIS'.

  • 20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 75 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 2 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test t-test t-test Chi-square test
14q gain 0 (0%) 158 0.346
(1.00) 		0.447
(1.00) 		0.0416
(1.00) 		1
(1.00) 		0.141
(1.00) 		0.252
(1.00) 		0.000166
(0.123) 		1
(1.00) 		0.0594
(1.00) 		0.422
(1.00)
20q gain 0 (0%) 30 0.035
(1.00) 		0.13
(1.00) 		0.686
(1.00) 		2.52e-05
(0.0186) 		0.308
(1.00) 		0.264
(1.00) 		0.741
(1.00) 		0.166
(1.00) 		0.884
(1.00) 		0.176
(1.00)
1p gain 0 (0%) 158 0.0147
(1.00) 		0.859
(1.00) 		0.332
(1.00) 		0.296
(1.00) 		1
(1.00) 		1
(1.00) 		0.00173
(1.00) 		1
(1.00) 		0.362
(1.00) 		0.173
(1.00)
1q gain 0 (0%) 135 0.413
(1.00) 		0.383
(1.00) 		0.53
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.829
(1.00) 		0.132
(1.00) 		0.53
(1.00) 		0.0596
(1.00) 		0.186
(1.00)
2p gain 0 (0%) 142 0.286
(1.00) 		0.451
(1.00) 		0.0073
(1.00) 		0.221
(1.00) 		1
(1.00) 		0.298
(1.00) 		0.603
(1.00) 		0.0697
(1.00) 		0.233
(1.00) 		0.664
(1.00)
2q gain 0 (0%) 141 0.154
(1.00) 		0.443
(1.00) 		0.0174
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.482
(1.00) 		0.0863
(1.00) 		0.796
(1.00) 		0.485
(1.00)
3p gain 0 (0%) 145 0.817
(1.00) 		0.748
(1.00) 		1
(1.00) 		0.363
(1.00) 		0.121
(1.00) 		0.0925
(1.00) 		0.0968
(1.00) 		0.762
(1.00) 		0.431
(1.00) 		0.741
(1.00)
3q gain 0 (0%) 139 0.51
(1.00) 		0.668
(1.00) 		0.27
(1.00) 		0.218
(1.00) 		0.203
(1.00) 		0.107
(1.00) 		0.0324
(1.00) 		0.301
(1.00) 		0.601
(1.00) 		0.861
(1.00)
4p gain 0 (0%) 158 0.571
(1.00) 		0.233
(1.00) 		0.626
(1.00) 		1
(1.00) 		1
(1.00) 		0.252
(1.00) 		0.992
(1.00) 		1
(1.00) 		0.00977
(1.00) 		0.0976
(1.00)
4q gain 0 (0%) 159 0.354
(1.00) 		0.251
(1.00) 		1
(1.00) 		1
(1.00) 		0.548
(1.00) 		0.87
(1.00) 		0.0749
(1.00) 		0.769
(1.00)
5p gain 0 (0%) 142 0.848
(1.00) 		0.0481
(1.00) 		0.638
(1.00) 		0.221
(1.00) 		0.552
(1.00) 		0.335
(1.00) 		0.221
(1.00) 		0.149
(1.00) 		0.16
(1.00) 		0.489
(1.00)
5q gain 0 (0%) 150 0.463
(1.00) 		0.0508
(1.00) 		1
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.214
(1.00) 		0.0536
(1.00) 		0.126
(1.00) 		0.331
(1.00) 		0.0969
(1.00)
6p gain 0 (0%) 135 0.863
(1.00) 		0.947
(1.00) 		0.834
(1.00) 		0.127
(1.00) 		0.0587
(1.00) 		0.374
(1.00) 		0.195
(1.00) 		0.0901
(1.00) 		0.509
(1.00) 		0.638
(1.00)
6q gain 0 (0%) 135 0.224
(1.00) 		0.356
(1.00) 		1
(1.00) 		0.128
(1.00) 		0.262
(1.00) 		0.135
(1.00) 		0.19
(1.00) 		0.103
(1.00) 		0.873
(1.00) 		0.325
(1.00)
7p gain 0 (0%) 72 0.33
(1.00) 		0.363
(1.00) 		0.874
(1.00) 		0.00225
(1.00) 		1
(1.00) 		0.804
(1.00) 		0.348
(1.00) 		0.234
(1.00) 		0.0672
(1.00) 		0.0268
(1.00)
7q gain 0 (0%) 83 0.418
(1.00) 		0.351
(1.00) 		1
(1.00) 		0.00232
(1.00) 		1
(1.00) 		0.443
(1.00) 		0.156
(1.00) 		0.182
(1.00) 		0.274
(1.00) 		0.00138
(1.00)
8p gain 0 (0%) 135 0.358
(1.00) 		0.15
(1.00) 		0.834
(1.00) 		1
(1.00) 		0.591
(1.00) 		0.713
(1.00) 		0.391
(1.00) 		0.0349
(1.00) 		0.184
(1.00) 		0.242
(1.00)
8q gain 0 (0%) 90 0.0676
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.145
(1.00) 		0.228
(1.00) 		0.0966
(1.00) 		0.321
(1.00) 		0.0128
(1.00) 		0.33
(1.00) 		0.0718
(1.00)
9p gain 0 (0%) 127 0.829
(1.00) 		0.296
(1.00) 		0.706
(1.00) 		1
(1.00) 		0.342
(1.00) 		0.56
(1.00) 		0.339
(1.00) 		0.863
(1.00) 		0.432
(1.00) 		0.182
(1.00)
9q gain 0 (0%) 136 0.354
(1.00) 		0.0862
(1.00) 		0.831
(1.00) 		1
(1.00) 		0.591
(1.00) 		0.9
(1.00) 		0.0937
(1.00) 		1
(1.00) 		0.76
(1.00) 		0.0125
(1.00)
10p gain 0 (0%) 154 0.996
(1.00) 		0.988
(1.00) 		0.471
(1.00) 		1
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.322
(1.00) 		0.61
(1.00) 		0.546
(1.00) 		0.933
(1.00)
10q gain 0 (0%) 158 0.333
(1.00) 		0.171
(1.00) 		0.0416
(1.00) 		1
(1.00) 		1
(1.00) 		0.655
(1.00) 		0.0846
(1.00) 		1
(1.00) 		0.424
(1.00) 		0.622
(1.00)
11p gain 0 (0%) 141 0.478
(1.00) 		0.195
(1.00) 		0.249
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.306
(1.00) 		0.49
(1.00) 		0.85
(1.00) 		0.949
(1.00) 		0.805
(1.00)
11q gain 0 (0%) 145 0.915
(1.00) 		0.0317
(1.00) 		0.8
(1.00) 		0.363
(1.00) 		1
(1.00) 		0.198
(1.00) 		0.179
(1.00) 		0.776
(1.00) 		0.0491
(1.00) 		0.63
(1.00)
12p gain 0 (0%) 134 0.997
(1.00) 		0.0797
(1.00) 		1
(1.00) 		1
(1.00) 		0.277
(1.00) 		0.565
(1.00) 		0.854
(1.00) 		0.691
(1.00) 		0.346
(1.00) 		0.665
(1.00)
12q gain 0 (0%) 143 0.504
(1.00) 		0.0205
(1.00) 		0.328
(1.00) 		1
(1.00) 		1
(1.00) 		0.93
(1.00) 		0.96
(1.00) 		0.806
(1.00) 		0.925
(1.00) 		0.814
(1.00)
13q gain 0 (0%) 60 0.0275
(1.00) 		0.489
(1.00) 		0.871
(1.00) 		0.000377
(0.278) 		0.671
(1.00) 		0.213
(1.00) 		0.223
(1.00) 		0.865
(1.00) 		0.695
(1.00) 		0.282
(1.00)
16p gain 0 (0%) 133 0.228
(1.00) 		0.636
(1.00) 		0.539
(1.00) 		0.129
(1.00) 		0.292
(1.00) 		0.441
(1.00) 		0.32
(1.00) 		0.588
(1.00) 		0.247
(1.00) 		0.637
(1.00)
16q gain 0 (0%) 132 0.865
(1.00) 		0.596
(1.00) 		1
(1.00) 		0.0747
(1.00) 		0.308
(1.00) 		0.158
(1.00) 		0.295
(1.00) 		0.813
(1.00) 		0.646
(1.00) 		0.739
(1.00)
17p gain 0 (0%) 159 0.257
(1.00) 		0.593
(1.00) 		1
(1.00) 		1
(1.00) 		0.548
(1.00) 		0.454
(1.00) 		0.563
(1.00)
17q gain 0 (0%) 144 0.626
(1.00) 		0.469
(1.00) 		0.621
(1.00) 		0.365
(1.00) 		1
(1.00) 		0.459
(1.00) 		0.544
(1.00) 		0.5
(1.00) 		0.506
(1.00) 		0.963
(1.00)
18p gain 0 (0%) 155 0.965
(1.00) 		0.622
(1.00) 		1
(1.00) 		0.463
(1.00) 		0.236
(1.00) 		0.194
(1.00) 		0.109
(1.00) 		0.487
(1.00) 		0.23
(1.00) 		0.195
(1.00)
18q gain 0 (0%) 158 0.747
(1.00) 		0.626
(1.00) 		1
(1.00) 		0.141
(1.00) 		0.0325
(1.00) 		0.000666
(0.492) 		0.35
(1.00) 		0.0888
(1.00)
19p gain 0 (0%) 142 0.864
(1.00) 		0.365
(1.00) 		0.473
(1.00) 		0.221
(1.00) 		1
(1.00) 		0.287
(1.00) 		0.964
(1.00) 		0.167
(1.00) 		0.832
(1.00) 		0.823
(1.00)
19q gain 0 (0%) 139 0.832
(1.00) 		0.645
(1.00) 		0.27
(1.00) 		0.218
(1.00) 		0.595
(1.00) 		0.148
(1.00) 		0.508
(1.00) 		0.0769
(1.00) 		0.0426
(1.00) 		0.769
(1.00)
20p gain 0 (0%) 67 0.862
(1.00) 		0.962
(1.00) 		0.2
(1.00) 		0.00182
(1.00) 		0.692
(1.00) 		0.714
(1.00) 		0.265
(1.00) 		0.172
(1.00) 		0.835
(1.00) 		0.0748
(1.00)
21q gain 0 (0%) 155 0.831
(1.00) 		0.0302
(1.00) 		0.703
(1.00) 		1
(1.00) 		1
(1.00) 		0.289
(1.00) 		0.0011
(0.813) 		0.553
(1.00) 		0.189
(1.00) 		0.888
(1.00)
22q gain 0 (0%) 157 0.0147
(1.00) 		0.781
(1.00) 		0.661
(1.00) 		1
(1.00) 		1
(1.00) 		0.737
(1.00) 		0.777
(1.00) 		0.413
(1.00) 		0.713
(1.00) 		0.52
(1.00)
Xq gain 0 (0%) 155 0.81
(1.00) 		0.718
(1.00) 		1
(1.00) 		0.463
(1.00) 		1
(1.00) 		0.289
(1.00) 		0.847
(1.00) 		0.206
(1.00) 		0.313
(1.00) 		0.788
(1.00)
1p loss 0 (0%) 141 0.802
(1.00) 		0.388
(1.00) 		0.105
(1.00) 		0.221
(1.00) 		0.571
(1.00) 		0.93
(1.00) 		0.838
(1.00) 		0.791
(1.00) 		0.936
(1.00) 		0.485
(1.00)
1q loss 0 (0%) 155 0.792
(1.00) 		0.629
(1.00) 		0.455
(1.00) 		1
(1.00) 		0.236
(1.00) 		1
(1.00) 		0.201
(1.00) 		0.61
(1.00) 		0.538
(1.00) 		0.0276
(1.00)
2p loss 0 (0%) 157 0.611
(1.00) 		0.0489
(1.00) 		0.661
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.737
(1.00) 		0.999
(1.00) 		0.413
(1.00) 		0.698
(1.00) 		0.961
(1.00)
3p loss 0 (0%) 154 0.851
(1.00) 		0.91
(1.00) 		0.292
(1.00) 		0.106
(1.00) 		0.266
(1.00) 		0.161
(1.00) 		0.934
(1.00) 		0.0274
(1.00) 		0.404
(1.00) 		0.669
(1.00)
3q loss 0 (0%) 158 0.879
(1.00) 		0.766
(1.00) 		0.626
(1.00) 		0.00175
(1.00) 		0.141
(1.00) 		0.548
(1.00) 		0.999
(1.00) 		0.041
(1.00) 		0.904
(1.00) 		0.811
(1.00)
4p loss 0 (0%) 123 0.278
(1.00) 		0.132
(1.00) 		0.581
(1.00) 		0.304
(1.00) 		0.151
(1.00) 		0.766
(1.00) 		0.643
(1.00) 		0.423
(1.00) 		0.169
(1.00) 		0.775
(1.00)
4q loss 0 (0%) 116 0.111
(1.00) 		0.306
(1.00) 		0.301
(1.00) 		0.188
(1.00) 		0.353
(1.00) 		0.787
(1.00) 		0.542
(1.00) 		0.583
(1.00) 		0.258
(1.00) 		0.767
(1.00)
5p loss 0 (0%) 151 0.153
(1.00) 		0.788
(1.00) 		0.114
(1.00) 		0.601
(1.00) 		0.349
(1.00) 		0.672
(1.00) 		0.0367
(1.00) 		1
(1.00) 		0.249
(1.00) 		0.437
(1.00)
5q loss 0 (0%) 139 0.582
(1.00) 		0.6
(1.00) 		0.27
(1.00) 		0.695
(1.00) 		0.00392
(1.00) 		0.414
(1.00) 		0.941
(1.00) 		0.368
(1.00) 		0.541
(1.00) 		0.449
(1.00)
6p loss 0 (0%) 154 0.098
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.106
(1.00) 		1
(1.00) 		1
(1.00) 		0.814
(1.00) 		0.126
(1.00) 		0.733
(1.00) 		0.238
(1.00)
6q loss 0 (0%) 148 0.629
(1.00) 		0.434
(1.00) 		0.577
(1.00) 		0.0643
(1.00) 		1
(1.00) 		0.738
(1.00) 		0.638
(1.00) 		0.419
(1.00) 		0.334
(1.00) 		0.209
(1.00)
8p loss 0 (0%) 106 0.272
(1.00) 		0.555
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.183
(1.00) 		0.427
(1.00) 		0.921
(1.00) 		0.53
(1.00) 		0.145
(1.00) 		0.598
(1.00)
8q loss 0 (0%) 159 0.53
(1.00) 		0.679
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.548
(1.00) 		0.997
(1.00) 		0.328
(1.00) 		0.237
(1.00) 		0.713
(1.00)
9p loss 0 (0%) 150 0.0165
(1.00) 		0.122
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.253
(1.00) 		0.951
(1.00) 		0.0169
(1.00) 		0.481
(1.00) 		0.804
(1.00)
9q loss 0 (0%) 151 0.00753
(1.00) 		0.677
(1.00) 		1
(1.00) 		0.592
(1.00) 		1
(1.00) 		0.672
(1.00) 		0.975
(1.00) 		0.0169
(1.00) 		0.209
(1.00) 		0.937
(1.00)
10p loss 0 (0%) 145 0.222
(1.00) 		0.00571
(1.00) 		1
(1.00) 		0.0377
(1.00) 		0.492
(1.00) 		0.78
(1.00) 		0.188
(1.00) 		0.63
(1.00) 		0.445
(1.00) 		0.607
(1.00)
10q loss 0 (0%) 141 0.537
(1.00) 		0.0482
(1.00) 		0.491
(1.00) 		0.0773
(1.00) 		0.571
(1.00) 		0.634
(1.00) 		0.754
(1.00) 		0.61
(1.00) 		0.564
(1.00) 		0.672
(1.00)
11p loss 0 (0%) 143 0.458
(1.00) 		0.578
(1.00) 		0.626
(1.00) 		0.046
(1.00) 		0.533
(1.00) 		0.698
(1.00) 		0.516
(1.00) 		0.271
(1.00) 		0.307
(1.00) 		0.167
(1.00)
11q loss 0 (0%) 139 0.344
(1.00) 		0.656
(1.00) 		0.508
(1.00) 		0.0137
(1.00) 		0.0379
(1.00) 		0.396
(1.00) 		0.21
(1.00) 		0.292
(1.00) 		0.869
(1.00) 		0.892
(1.00)
12p loss 0 (0%) 150 0.175
(1.00) 		0.642
(1.00) 		0.0397
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.496
(1.00) 		0.0684
(1.00) 		1
(1.00) 		0.467
(1.00) 		0.869
(1.00)
12q loss 0 (0%) 154 0.0958
(1.00) 		0.466
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.245
(1.00) 		0.651
(1.00) 		0.487
(1.00) 		0.973
(1.00) 		0.969
(1.00)
13q loss 0 (0%) 157 0.98
(1.00) 		1
(1.00) 		0.357
(1.00) 		1
(1.00) 		0.102
(1.00) 		0.796
(1.00) 		1
(1.00) 		0.438
(1.00) 		0.577
(1.00)
14q loss 0 (0%) 111 0.627
(1.00) 		0.881
(1.00) 		0.735
(1.00) 		0.00981
(1.00) 		1
(1.00) 		0.503
(1.00) 		0.496
(1.00) 		0.895
(1.00) 		0.395
(1.00) 		0.398
(1.00)
15q loss 0 (0%) 104 0.0699
(1.00) 		0.415
(1.00) 		0.511
(1.00) 		1
(1.00) 		0.668
(1.00) 		0.923
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.0597
(1.00) 		0.236
(1.00)
16p loss 0 (0%) 156 0.238
(1.00) 		0.413
(1.00) 		0.357
(1.00) 		1
(1.00) 		1
(1.00) 		0.909
(1.00) 		1
(1.00) 		0.274
(1.00) 		0.216
(1.00)
16q loss 0 (0%) 152 0.879
(1.00) 		0.532
(1.00) 		1
(1.00) 		0.553
(1.00) 		0.322
(1.00) 		1
(1.00) 		0.767
(1.00) 		1
(1.00) 		0.367
(1.00) 		0.657
(1.00)
17p loss 0 (0%) 73 0.446
(1.00) 		0.0299
(1.00) 		0.527
(1.00) 		0.572
(1.00) 		0.691
(1.00) 		0.435
(1.00) 		0.785
(1.00) 		0.482
(1.00) 		0.628
(1.00) 		0.694
(1.00)
17q loss 0 (0%) 147 0.459
(1.00) 		0.864
(1.00) 		0.788
(1.00) 		1
(1.00) 		0.0967
(1.00) 		1
(1.00) 		0.52
(1.00) 		0.596
(1.00) 		0.0679
(1.00) 		0.401
(1.00)
18p loss 0 (0%) 48 0.643
(1.00) 		0.0737
(1.00) 		0.863
(1.00) 		0.00925
(1.00) 		1
(1.00) 		0.321
(1.00) 		0.689
(1.00) 		0.75
(1.00) 		0.429
(1.00) 		0.445
(1.00)
18q loss 0 (0%) 36 0.403
(1.00) 		0.0453
(1.00) 		0.448
(1.00) 		0.482
(1.00) 		0.615
(1.00) 		0.603
(1.00) 		0.456
(1.00) 		0.847
(1.00) 		0.559
(1.00) 		0.389
(1.00)
19p loss 0 (0%) 155 0.0855
(1.00) 		0.794
(1.00) 		0.703
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.867
(1.00) 		1
(1.00) 		0.504
(1.00) 		0.14
(1.00)
19q loss 0 (0%) 155 0.0445
(1.00) 		0.403
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.799
(1.00) 		0.99
(1.00) 		1
(1.00) 		0.153
(1.00) 		0.00675
(1.00)
20p loss 0 (0%) 144 0.996
(1.00) 		0.689
(1.00) 		0.803
(1.00) 		0.636
(1.00) 		1
(1.00) 		0.923
(1.00) 		0.989
(1.00) 		0.338
(1.00) 		0.537
(1.00) 		0.00467
(1.00)
21q loss 0 (0%) 119 0.159
(1.00) 		0.807
(1.00) 		0.476
(1.00) 		0.517
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.217
(1.00) 		0.935
(1.00) 		0.0676
(1.00) 		0.31
(1.00)
22q loss 0 (0%) 120 0.0258
(1.00) 		0.284
(1.00) 		0.475
(1.00) 		0.745
(1.00) 		0.181
(1.00) 		0.598
(1.00) 		0.0911
(1.00) 		0.662
(1.00) 		0.998
(1.00) 		0.313
(1.00)
Xq loss 0 (0%) 156 0.519
(1.00) 		0.0974
(1.00) 		0.689
(1.00) 		1
(1.00) 		1
(1.00) 		0.221
(1.00) 		0.858
(1.00) 		0.158
(1.00) 		0.641
(1.00) 		0.765
(1.00)
'14q gain' versus 'LYMPH.NODE.METASTASIS'

P value = 0.000166 (Chi-square test), Q value = 0.12

Table S1.  Gene #26: '14q gain' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 83 35 4 5 1 23 2 7 1
14Q GAIN CNV 1 1 0 2 0 0 0 0 0
14Q GAIN WILD-TYPE 82 34 4 3 1 23 2 7 1

Figure S1.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 2.52e-05 (Fisher's exact test), Q value = 0.019

Table S2.  Gene #36: '20q gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 143 13
20Q GAIN CNV 124 4
20Q GAIN WILD-TYPE 19 9

Figure S2.  Get High-res Image Gene #36: '20q gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Clinical data file = READ-TP.clin.merged.picked.txt

  • Number of patients = 162

  • Number of significantly arm-level cnvs = 75

  • Number of selected clinical features = 11

  • Exclude genes 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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] 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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