Correlation between copy number variations of arm-level result and selected clinical features
Stomach Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1RF5S17
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Stomach Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1RF5S17
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 74 arm-level results and 11 clinical features across 180 patients, 4 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 2q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 3q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 12p loss cnv correlated to 'PATHOLOGY.N'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 74 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 4 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-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 Fisher's exact test t-test
2p gain 0 (0%) 168 0.641
(1.00) 		0.198
(1.00) 		0.765
(1.00) 		0.627
(1.00) 		0.113
(1.00) 		0.256
(1.00) 		1
(1.00) 		0.053
(1.00) 		1
(1.00) 		0.604
(1.00) 		3.16e-06
(0.0025)
2q gain 0 (0%) 166 0.314
(1.00) 		0.511
(1.00) 		0.785
(1.00) 		0.475
(1.00) 		0.271
(1.00) 		0.256
(1.00) 		0.804
(1.00) 		0.256
(1.00) 		1
(1.00) 		0.93
(1.00) 		4.34e-08
(3.43e-05)
3q loss 0 (0%) 171 0.666
(1.00) 		0.904
(1.00) 		0.319
(1.00) 		0.414
(1.00) 		1
(1.00) 		0.874
(1.00) 		1
(1.00) 		0.81
(1.00) 		1
(1.00) 		0.623
(1.00) 		0.000139
(0.109)
12p loss 0 (0%) 166 0.142
(1.00) 		0.371
(1.00) 		0.785
(1.00) 		0.577
(1.00) 		0.164
(1.00) 		0.000188
(0.148) 		0.35
(1.00) 		0.000576
(0.453) 		0.336
(1.00) 		0.787
(1.00) 		0.518
(1.00)
1p gain 0 (0%) 170 0.658
(1.00) 		0.956
(1.00) 		0.742
(1.00) 		0.756
(1.00) 		0.652
(1.00) 		0.643
(1.00) 		0.337
(1.00) 		0.547
(1.00) 		1
(1.00) 		0.0851
(1.00) 		0.643
(1.00)
1q gain 0 (0%) 155 0.995
(1.00) 		0.867
(1.00) 		0.51
(1.00) 		0.542
(1.00) 		0.761
(1.00) 		0.276
(1.00) 		0.36
(1.00) 		0.485
(1.00) 		0.142
(1.00) 		0.608
(1.00) 		0.584
(1.00)
3p gain 0 (0%) 177 0.723
(1.00) 		1
(1.00) 		0.935
(1.00) 		0.588
(1.00) 		0.859
(1.00) 		1
(1.00) 		0.614
(1.00) 		1
(1.00) 		0.166
(1.00) 		0.901
(1.00)
3q gain 0 (0%) 165 0.341
(1.00) 		0.0158
(1.00) 		0.0294
(1.00) 		0.607
(1.00) 		0.711
(1.00) 		0.849
(1.00) 		0.383
(1.00) 		1
(1.00) 		1
(1.00) 		0.715
(1.00) 		0.647
(1.00)
4p gain 0 (0%) 177 0.118
(1.00) 		0.276
(1.00) 		0.131
(1.00) 		0.859
(1.00) 		1
(1.00) 		0.302
(1.00) 		1
(1.00) 		0.235
(1.00)
5p gain 0 (0%) 152 0.886
(1.00) 		0.396
(1.00) 		0.679
(1.00) 		0.276
(1.00) 		0.476
(1.00) 		0.939
(1.00) 		0.352
(1.00) 		0.064
(1.00) 		0.575
(1.00) 		0.261
(1.00) 		0.243
(1.00)
5q gain 0 (0%) 173 0.233
(1.00) 		0.787
(1.00) 		0.704
(1.00) 		0.0999
(1.00) 		0.899
(1.00) 		0.388
(1.00) 		1
(1.00) 		0.408
(1.00) 		1
(1.00) 		0.83
(1.00) 		0.592
(1.00)
6p gain 0 (0%) 163 0.655
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.0769
(1.00) 		0.552
(1.00) 		0.861
(1.00) 		0.51
(1.00) 		0.395
(1.00) 		0.782
(1.00) 		0.0419
(1.00)
6q gain 0 (0%) 166 0.29
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.839
(1.00) 		0.271
(1.00) 		0.592
(1.00) 		0.35
(1.00) 		0.782
(1.00) 		0.336
(1.00) 		0.447
(1.00) 		0.0424
(1.00)
7p gain 0 (0%) 121 0.384
(1.00) 		0.0948
(1.00) 		0.261
(1.00) 		0.0899
(1.00) 		0.714
(1.00) 		0.373
(1.00) 		0.764
(1.00) 		0.327
(1.00) 		0.663
(1.00) 		0.582
(1.00) 		0.924
(1.00)
7q gain 0 (0%) 129 0.563
(1.00) 		0.0224
(1.00) 		0.5
(1.00) 		0.26
(1.00) 		0.689
(1.00) 		0.492
(1.00) 		0.272
(1.00) 		0.278
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.852
(1.00)
8p gain 0 (0%) 125 0.879
(1.00) 		0.00576
(1.00) 		0.103
(1.00) 		0.178
(1.00) 		0.391
(1.00) 		0.643
(1.00) 		0.138
(1.00) 		0.623
(1.00) 		0.168
(1.00) 		0.177
(1.00) 		0.553
(1.00)
8q gain 0 (0%) 104 0.329
(1.00) 		0.00678
(1.00) 		0.169
(1.00) 		0.184
(1.00) 		0.201
(1.00) 		0.235
(1.00) 		0.0464
(1.00) 		0.262
(1.00) 		0.651
(1.00) 		0.055
(1.00) 		0.99
(1.00)
9p gain 0 (0%) 165 0.905
(1.00) 		0.715
(1.00) 		0.593
(1.00) 		0.782
(1.00) 		0.0726
(1.00) 		0.0993
(1.00) 		1
(1.00) 		0.0135
(1.00) 		0.356
(1.00) 		1
(1.00) 		0.4
(1.00)
9q gain 0 (0%) 160 0.96
(1.00) 		0.975
(1.00) 		1
(1.00) 		0.884
(1.00) 		0.258
(1.00) 		0.0944
(1.00) 		0.626
(1.00) 		0.271
(1.00) 		0.449
(1.00) 		1
(1.00) 		0.754
(1.00)
10p gain 0 (0%) 151 0.806
(1.00) 		0.345
(1.00) 		0.839
(1.00) 		0.378
(1.00) 		0.0581
(1.00) 		0.82
(1.00) 		0.378
(1.00) 		0.0914
(1.00) 		1
(1.00) 		0.428
(1.00) 		0.735
(1.00)
10q gain 0 (0%) 165 0.704
(1.00) 		0.617
(1.00) 		0.784
(1.00) 		0.745
(1.00) 		0.323
(1.00) 		0.948
(1.00) 		0.57
(1.00) 		0.826
(1.00) 		1
(1.00) 		0.584
(1.00) 		0.812
(1.00)
11p gain 0 (0%) 173 0.441
(1.00) 		0.375
(1.00) 		0.704
(1.00) 		0.611
(1.00) 		0.379
(1.00) 		0.228
(1.00) 		1
(1.00) 		0.218
(1.00) 		1
(1.00) 		0.352
(1.00) 		0.221
(1.00)
11q gain 0 (0%) 168 0.158
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.522
(1.00) 		0.647
(1.00) 		0.836
(1.00) 		0.749
(1.00) 		0.712
(1.00) 		1
(1.00) 		0.644
(1.00) 		0.012
(1.00)
12p gain 0 (0%) 160 0.338
(1.00) 		0.344
(1.00) 		0.225
(1.00) 		0.647
(1.00) 		0.235
(1.00) 		0.754
(1.00) 		0.103
(1.00) 		0.595
(1.00) 		1
(1.00) 		0.448
(1.00) 		0.337
(1.00)
12q gain 0 (0%) 165 0.787
(1.00) 		0.0171
(1.00) 		0.784
(1.00) 		0.0875
(1.00) 		0.467
(1.00) 		0.209
(1.00) 		0.638
(1.00) 		0.66
(1.00) 		0.356
(1.00) 		0.671
(1.00) 		0.661
(1.00)
13q gain 0 (0%) 144 0.508
(1.00) 		0.855
(1.00) 		0.705
(1.00) 		0.498
(1.00) 		0.876
(1.00) 		0.404
(1.00) 		0.642
(1.00) 		0.843
(1.00) 		1
(1.00) 		0.865
(1.00) 		0.456
(1.00)
14q gain 0 (0%) 177 0.0394
(1.00) 		0.669
(1.00) 		0.0624
(1.00) 		0.964
(1.00) 		1
(1.00) 		0.0305
(1.00)
15q gain 0 (0%) 172 0.14
(1.00) 		0.635
(1.00) 		0.0224
(1.00) 		0.414
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.61
(1.00) 		0.811
(1.00) 		1
(1.00) 		0.83
(1.00) 		0.69
(1.00)
16p gain 0 (0%) 167 0.511
(1.00) 		0.956
(1.00) 		0.567
(1.00) 		0.75
(1.00) 		0.0566
(1.00) 		0.0889
(1.00) 		0.089
(1.00) 		0.00694
(1.00) 		0.316
(1.00) 		0.928
(1.00) 		0.327
(1.00)
16q gain 0 (0%) 170 0.554
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.907
(1.00) 		0.00412
(1.00) 		0.512
(1.00) 		0.161
(1.00) 		0.0218
(1.00) 		1
(1.00) 		0.882
(1.00) 		0.894
(1.00)
17p gain 0 (0%) 174 0.0114
(1.00) 		0.614
(1.00) 		0.685
(1.00) 		0.782
(1.00) 		0.386
(1.00) 		0.0114
(1.00) 		0.0193
(1.00) 		0.0609
(1.00) 		1
(1.00) 		0.0136
(1.00) 		0.224
(1.00)
17q gain 0 (0%) 168 0.31
(1.00) 		0.341
(1.00) 		0.765
(1.00) 		0.9
(1.00) 		0.334
(1.00) 		0.0809
(1.00) 		0.0208
(1.00) 		0.264
(1.00) 		1
(1.00) 		0.0647
(1.00) 		0.283
(1.00)
18p gain 0 (0%) 162 0.767
(1.00) 		0.256
(1.00) 		0.801
(1.00) 		0.614
(1.00) 		0.948
(1.00) 		0.0681
(1.00) 		0.57
(1.00) 		0.567
(1.00) 		0.413
(1.00) 		0.513
(1.00) 		0.351
(1.00)
18q gain 0 (0%) 170 0.703
(1.00) 		0.775
(1.00) 		0.524
(1.00) 		0.57
(1.00) 		0.269
(1.00) 		0.772
(1.00) 		0.119
(1.00) 		0.937
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.757
(1.00)
19p gain 0 (0%) 170 0.88
(1.00) 		0.267
(1.00) 		0.0154
(1.00) 		0.445
(1.00) 		0.754
(1.00) 		0.0513
(1.00) 		0.0312
(1.00) 		0.0368
(1.00) 		1
(1.00) 		0.00108
(0.847) 		0.0332
(1.00)
19q gain 0 (0%) 161 0.209
(1.00) 		0.276
(1.00) 		0.136
(1.00) 		0.896
(1.00) 		0.229
(1.00) 		0.202
(1.00) 		0.184
(1.00) 		0.0218
(1.00) 		0.431
(1.00) 		0.0145
(1.00) 		0.0696
(1.00)
20p gain 0 (0%) 106 0.0917
(1.00) 		0.164
(1.00) 		0.00336
(1.00) 		0.457
(1.00) 		0.342
(1.00) 		0.592
(1.00) 		0.118
(1.00) 		0.0869
(1.00) 		0.65
(1.00) 		0.229
(1.00) 		0.835
(1.00)
20q gain 0 (0%) 90 0.0657
(1.00) 		0.0968
(1.00) 		0.0037
(1.00) 		0.149
(1.00) 		0.0771
(1.00) 		0.509
(1.00) 		0.0402
(1.00) 		0.0392
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.197
(1.00)
22q gain 0 (0%) 177 0.748
(1.00) 		0.353
(1.00) 		1
(1.00) 		0.964
(1.00) 		1
(1.00) 		0.434
(1.00) 		1
(1.00) 		0.302
(1.00) 		1
(1.00) 		1
(1.00)
1p loss 0 (0%) 170 0.194
(1.00) 		0.318
(1.00) 		0.202
(1.00) 		0.175
(1.00) 		0.588
(1.00) 		0.104
(1.00) 		0.00746
(1.00) 		0.0197
(1.00) 		1
(1.00) 		0.0107
(1.00) 		0.431
(1.00)
2p loss 0 (0%) 177 0.565
(1.00) 		0.0815
(1.00) 		0.235
(1.00)
3p loss 0 (0%) 165 0.824
(1.00) 		0.446
(1.00) 		0.784
(1.00) 		0.448
(1.00) 		0.94
(1.00) 		0.866
(1.00) 		1
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.312
(1.00) 		0.0325
(1.00)
4p loss 0 (0%) 150 0.441
(1.00) 		0.318
(1.00) 		0.839
(1.00) 		0.154
(1.00) 		0.262
(1.00) 		0.925
(1.00) 		0.33
(1.00) 		0.262
(1.00) 		0.194
(1.00) 		0.152
(1.00) 		0.146
(1.00)
4q loss 0 (0%) 152 0.938
(1.00) 		0.94
(1.00) 		0.53
(1.00) 		0.0656
(1.00) 		0.101
(1.00) 		0.883
(1.00) 		0.698
(1.00) 		0.74
(1.00) 		0.173
(1.00) 		0.233
(1.00) 		0.19
(1.00)
5p loss 0 (0%) 170 0.835
(1.00) 		0.377
(1.00) 		0.742
(1.00) 		0.14
(1.00) 		0.762
(1.00) 		0.136
(1.00) 		1
(1.00) 		0.411
(1.00) 		1
(1.00) 		1
(1.00) 		0.761
(1.00)
5q loss 0 (0%) 160 0.291
(1.00) 		0.867
(1.00) 		0.225
(1.00) 		0.052
(1.00) 		0.139
(1.00) 		0.85
(1.00) 		0.346
(1.00) 		0.219
(1.00) 		0.449
(1.00) 		0.22
(1.00) 		0.517
(1.00)
6p loss 0 (0%) 171 0.751
(1.00) 		0.286
(1.00) 		1
(1.00) 		0.0696
(1.00) 		0.291
(1.00) 		0.0452
(1.00) 		0.337
(1.00) 		0.339
(1.00) 		1
(1.00) 		0.882
(1.00) 		0.429
(1.00)
6q loss 0 (0%) 166 0.732
(1.00) 		0.568
(1.00) 		0.411
(1.00) 		0.481
(1.00) 		0.413
(1.00) 		0.364
(1.00) 		0.804
(1.00) 		0.064
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.616
(1.00)
7p loss 0 (0%) 177 0.217
(1.00) 		0.238
(1.00) 		0.276
(1.00) 		0.795
(1.00) 		0.0409
(1.00) 		0.0801
(1.00) 		1
(1.00) 		0.54
(1.00) 		1
(1.00) 		1
(1.00)
7q loss 0 (0%) 174 0.211
(1.00) 		0.26
(1.00) 		0.0825
(1.00) 		0.474
(1.00) 		0.27
(1.00) 		0.521
(1.00) 		1
(1.00) 		0.93
(1.00) 		1
(1.00) 		0.802
(1.00) 		0.395
(1.00)
8p loss 0 (0%) 161 0.721
(1.00) 		0.293
(1.00) 		0.47
(1.00) 		0.014
(1.00) 		0.215
(1.00) 		0.131
(1.00) 		0.089
(1.00) 		0.393
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.00367
(1.00)
8q loss 0 (0%) 174 0.773
(1.00) 		0.874
(1.00) 		1
(1.00) 		0.00979
(1.00) 		1
(1.00) 		1
(1.00) 		0.643
(1.00) 		0.000804
(0.631)
9p loss 0 (0%) 148 0.0648
(1.00) 		0.933
(1.00) 		0.553
(1.00) 		0.192
(1.00) 		0.0138
(1.00) 		0.82
(1.00) 		0.479
(1.00) 		0.628
(1.00) 		1
(1.00) 		0.737
(1.00) 		0.371
(1.00)
9q loss 0 (0%) 167 0.62
(1.00) 		0.363
(1.00) 		0.248
(1.00) 		0.277
(1.00) 		0.0103
(1.00) 		0.321
(1.00) 		0.749
(1.00) 		0.631
(1.00) 		0.316
(1.00) 		0.644
(1.00) 		0.263
(1.00)
10p loss 0 (0%) 166 0.177
(1.00) 		0.725
(1.00) 		0.411
(1.00) 		0.0441
(1.00) 		0.178
(1.00) 		0.343
(1.00) 		0.785
(1.00) 		0.494
(1.00) 		0.0492
(1.00) 		0.629
(1.00) 		0.689
(1.00)
10q loss 0 (0%) 169 0.22
(1.00) 		0.232
(1.00) 		0.757
(1.00) 		0.0326
(1.00) 		0.501
(1.00) 		0.554
(1.00) 		0.749
(1.00) 		0.201
(1.00) 		0.273
(1.00) 		1
(1.00) 		0.832
(1.00)
11p loss 0 (0%) 168 0.392
(1.00) 		0.0898
(1.00) 		1
(1.00) 		0.218
(1.00) 		0.164
(1.00) 		0.896
(1.00) 		0.22
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.0437
(1.00) 		0.405
(1.00)
11q loss 0 (0%) 169 0.0781
(1.00) 		0.602
(1.00) 		0.204
(1.00) 		0.638
(1.00) 		0.297
(1.00) 		0.672
(1.00) 		0.451
(1.00) 		0.574
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.353
(1.00)
12q loss 0 (0%) 171 0.328
(1.00) 		0.575
(1.00) 		0.319
(1.00) 		0.752
(1.00) 		0.331
(1.00) 		0.026
(1.00) 		1
(1.00) 		0.111
(1.00) 		1
(1.00) 		1
(1.00) 		0.955
(1.00)
13q loss 0 (0%) 175 0.719
(1.00) 		1
(1.00) 		0.424
(1.00) 		0.568
(1.00) 		0.316
(1.00) 		0.61
(1.00) 		0.594
(1.00) 		0.133
(1.00) 		0.0754
(1.00)
14q loss 0 (0%) 164 0.605
(1.00) 		0.053
(1.00) 		0.596
(1.00) 		0.222
(1.00) 		0.921
(1.00) 		0.701
(1.00) 		0.766
(1.00) 		0.926
(1.00) 		1
(1.00) 		0.847
(1.00) 		0.229
(1.00)
15q loss 0 (0%) 164 0.969
(1.00) 		0.24
(1.00) 		0.793
(1.00) 		0.0627
(1.00) 		0.151
(1.00) 		0.278
(1.00) 		0.804
(1.00) 		0.41
(1.00) 		0.0634
(1.00) 		0.722
(1.00) 		0.551
(1.00)
16p loss 0 (0%) 164 0.528
(1.00) 		0.718
(1.00) 		0.596
(1.00) 		0.0846
(1.00) 		0.297
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.891
(1.00) 		0.376
(1.00) 		0.328
(1.00) 		0.629
(1.00)
16q loss 0 (0%) 161 0.511
(1.00) 		0.819
(1.00) 		0.47
(1.00) 		0.229
(1.00) 		0.363
(1.00) 		0.164
(1.00) 		1
(1.00) 		0.972
(1.00) 		0.431
(1.00) 		0.424
(1.00) 		0.315
(1.00)
17p loss 0 (0%) 144 0.705
(1.00) 		0.453
(1.00) 		0.254
(1.00) 		0.0247
(1.00) 		0.283
(1.00) 		0.467
(1.00) 		0.771
(1.00) 		0.561
(1.00) 		0.0553
(1.00) 		0.158
(1.00) 		0.892
(1.00)
17q loss 0 (0%) 169 0.537
(1.00) 		0.553
(1.00) 		0.757
(1.00) 		0.0583
(1.00) 		0.769
(1.00) 		0.494
(1.00) 		0.208
(1.00) 		0.558
(1.00) 		0.273
(1.00) 		0.402
(1.00) 		0.0822
(1.00)
18p loss 0 (0%) 166 0.416
(1.00) 		0.898
(1.00) 		0.785
(1.00) 		0.952
(1.00) 		0.469
(1.00) 		0.263
(1.00) 		0.681
(1.00) 		0.456
(1.00) 		1
(1.00) 		0.279
(1.00) 		0.805
(1.00)
18q loss 0 (0%) 152 0.328
(1.00) 		0.966
(1.00) 		1
(1.00) 		0.743
(1.00) 		0.711
(1.00) 		0.14
(1.00) 		0.159
(1.00) 		0.478
(1.00) 		1
(1.00) 		0.0195
(1.00) 		0.215
(1.00)
19p loss 0 (0%) 160 0.952
(1.00) 		0.692
(1.00) 		0.469
(1.00) 		0.618
(1.00) 		0.734
(1.00) 		0.29
(1.00) 		0.754
(1.00) 		0.664
(1.00) 		1
(1.00) 		0.426
(1.00) 		0.444
(1.00)
19q loss 0 (0%) 166 0.924
(1.00) 		0.0712
(1.00) 		0.411
(1.00) 		0.676
(1.00) 		0.712
(1.00) 		0.168
(1.00) 		0.681
(1.00) 		0.22
(1.00) 		1
(1.00) 		0.52
(1.00) 		0.426
(1.00)
20p loss 0 (0%) 175 0.325
(1.00) 		0.786
(1.00) 		0.084
(1.00) 		0.754
(1.00) 		0.101
(1.00) 		0.261
(1.00) 		0.122
(1.00) 		0.122
(1.00) 		0.133
(1.00) 		0.00523
(1.00) 		0.528
(1.00)
21q loss 0 (0%) 145 0.662
(1.00) 		0.308
(1.00) 		0.848
(1.00) 		0.755
(1.00) 		0.795
(1.00) 		0.862
(1.00) 		0.619
(1.00) 		0.762
(1.00) 		1
(1.00) 		0.349
(1.00) 		0.188
(1.00)
22q loss 0 (0%) 155 0.311
(1.00) 		0.848
(1.00) 		1
(1.00) 		0.429
(1.00) 		0.874
(1.00) 		0.523
(1.00) 		0.885
(1.00) 		0.732
(1.00) 		0.531
(1.00) 		0.493
(1.00) 		0.33
(1.00)
Xq loss 0 (0%) 172 0.193
(1.00) 		0.123
(1.00) 		1
(1.00) 		0.779
(1.00) 		0.435
(1.00) 		0.261
(1.00) 		1
(1.00) 		0.386
(1.00) 		0.205
(1.00) 		0.049
(1.00) 		0.998
(1.00)
'2p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.16e-06 (t-test), Q value = 0.0025

Table S1.  Gene #3: '2p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 136 4.0 (5.6)
2P GAIN CNV 8 0.6 (1.2)
2P GAIN WILD-TYPE 128 4.2 (5.7)

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'2q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.34e-08 (t-test), Q value = 3.4e-05

Table S2.  Gene #4: '2q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 136 4.0 (5.6)
2Q GAIN CNV 10 0.5 (1.1)
2Q GAIN WILD-TYPE 126 4.3 (5.8)

Figure S2.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'3q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000139 (t-test), Q value = 0.11

Table S3.  Gene #41: '3q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 136 4.0 (5.6)
3Q LOSS CNV 7 1.1 (1.2)
3Q LOSS WILD-TYPE 129 4.2 (5.7)

Figure S3.  Get High-res Image Gene #41: '3q loss' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'12p loss' versus 'PATHOLOGY.N'

P value = 0.000188 (Fisher's exact test), Q value = 0.15

Table S4.  Gene #58: '12p loss' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2 N3
ALL 44 49 23 15
12P LOSS CNV 10 0 0 1
12P LOSS WILD-TYPE 34 49 23 14

Figure S4.  Get High-res Image Gene #58: '12p loss' versus Clinical Feature #6: 'PATHOLOGY.N'

Methods & Data
Input

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

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

  • Number of patients = 180

  • Number of significantly arm-level cnvs = 74

  • 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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