Correlation between copy number variation genes (focal) and selected clinical features
Colon Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C16M34TP
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 variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C16M34TP
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 68 arm-level results and 11 clinical features across 413 patients, 22 significant findings detected with Q value < 0.25.

  • Amp Peak 11(13q12.13) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 12(13q22.1) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 13(16p11.2) cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • Amp Peak 14(16q12.1) cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • Amp Peak 22(20q11.21) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 23(20q12) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 24(20q13.32) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 1(1p36.11) cnv correlated to 'DISTANT.METASTASIS'.

  • Del Peak 9(4p16.2) cnv correlated to 'Time to Death' and 'DISTANT.METASTASIS'.

  • Del Peak 19(8p22) cnv correlated to 'LYMPH.NODE.METASTASIS' and 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 28(13q14.13) cnv correlated to 'DISTANT.METASTASIS'.

  • Del Peak 35(17p12) cnv correlated to 'HISTOLOGICAL.TYPE',  'LYMPH.NODE.METASTASIS',  'NUMBER.OF.LYMPH.NODES', and 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 37(18p11.31) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 38(18q12.2) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 39(18q21.2) cnv correlated to 'HISTOLOGICAL.TYPE' and 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 40(18q22.1) 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 68 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 22 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 Chi-square test Chi-square test Fisher's exact test t-test t-test Chi-square test
Del Peak 35(17p12) 0 (0%) 184 0.34
(1.00) 		0.0108
(1.00) 		0.427
(1.00) 		3.61e-06
(0.00243) 		0.257
(1.00) 		0.0157
(1.00) 		0.000291
(0.192) 		0.26
(1.00) 		6.46e-05
(0.0431) 		4.8e-05
(0.0321)
Del Peak 9(4p16 2) 0 (0%) 292 0.000312
(0.206) 		0.609
(1.00) 		0.665
(1.00) 		0.036
(1.00) 		0.0247
(1.00) 		0.000248
(0.164) 		0.0188
(1.00) 		0.0286
(1.00) 		0.0076
(1.00) 		0.00139
(0.893)
Del Peak 19(8p22) 0 (0%) 228 0.417
(1.00) 		0.104
(1.00) 		0.236
(1.00) 		0.0186
(1.00) 		0.589
(1.00) 		0.00127
(0.815) 		7.07e-05
(0.0472) 		0.043
(1.00) 		0.00105
(0.679) 		0.000229
(0.152)
Del Peak 39(18q21 2) 0 (0%) 153 0.407
(1.00) 		0.0992
(1.00) 		0.125
(1.00) 		4.16e-09
(2.81e-06) 		0.299
(1.00) 		0.00582
(1.00) 		0.00294
(1.00) 		0.139
(1.00) 		0.0205
(1.00) 		0.000167
(0.111)
Amp Peak 11(13q12 13) 0 (0%) 163 0.294
(1.00) 		0.522
(1.00) 		0.84
(1.00) 		9.63e-07
(0.000651) 		0.282
(1.00) 		0.0049
(1.00) 		0.0405
(1.00) 		0.0357
(1.00) 		0.0534
(1.00) 		0.00613
(1.00)
Amp Peak 12(13q22 1) 0 (0%) 159 0.0728
(1.00) 		0.565
(1.00) 		0.312
(1.00) 		8.61e-06
(0.00578) 		0.288
(1.00) 		0.0073
(1.00) 		0.00901
(1.00) 		0.0724
(1.00) 		0.0816
(1.00) 		0.00684
(1.00)
Amp Peak 13(16p11 2) 0 (0%) 297 0.436
(1.00) 		0.0688
(1.00) 		0.512
(1.00) 		0.00867
(1.00) 		1
(1.00) 		0.316
(1.00) 		0.00398
(1.00) 		0.78
(1.00) 		0.00552
(1.00) 		0.00036
(0.237)
Amp Peak 14(16q12 1) 0 (0%) 311 0.367
(1.00) 		0.0166
(1.00) 		0.425
(1.00) 		0.0165
(1.00) 		0.574
(1.00) 		0.177
(1.00) 		0.0033
(1.00) 		0.775
(1.00) 		0.0162
(1.00) 		8.95e-05
(0.0596)
Amp Peak 22(20q11 21) 0 (0%) 117 0.434
(1.00) 		0.474
(1.00) 		0.326
(1.00) 		7.35e-06
(0.00494) 		0.562
(1.00) 		0.0105
(1.00) 		0.225
(1.00) 		0.145
(1.00) 		0.0736
(1.00) 		0.00283
(1.00)
Amp Peak 23(20q12) 0 (0%) 116 0.366
(1.00) 		0.51
(1.00) 		0.274
(1.00) 		1.31e-06
(0.000881) 		0.563
(1.00) 		0.00491
(1.00) 		0.254
(1.00) 		0.146
(1.00) 		0.0994
(1.00) 		0.00114
(0.737)
Amp Peak 24(20q13 32) 0 (0%) 113 0.372
(1.00) 		0.537
(1.00) 		0.376
(1.00) 		4.75e-06
(0.0032) 		0.565
(1.00) 		0.00689
(1.00) 		0.171
(1.00) 		0.146
(1.00) 		0.0271
(1.00) 		0.00161
(1.00)
Del Peak 1(1p36 11) 0 (0%) 263 0.0234
(1.00) 		0.144
(1.00) 		0.474
(1.00) 		0.00364
(1.00) 		1
(1.00) 		0.000113
(0.0754) 		0.0315
(1.00) 		0.0792
(1.00) 		0.0061
(1.00) 		0.00369
(1.00)
Del Peak 28(13q14 13) 0 (0%) 395 0.308
(1.00) 		0.279
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		4.21e-05
(0.0282) 		0.00704
(1.00) 		0.75
(1.00) 		0.223
(1.00) 		0.000442
(0.29)
Del Peak 37(18p11 31) 0 (0%) 193 0.874
(1.00) 		0.0199
(1.00) 		1
(1.00) 		8.95e-11
(6.09e-08) 		0.251
(1.00) 		0.00359
(1.00) 		0.389
(1.00) 		0.0293
(1.00) 		0.375
(1.00) 		0.0143
(1.00)
Del Peak 38(18q12 2) 0 (0%) 166 0.993
(1.00) 		0.0542
(1.00) 		0.365
(1.00) 		3.31e-10
(2.25e-07) 		0.277
(1.00) 		0.0119
(1.00) 		0.0437
(1.00) 		0.149
(1.00) 		0.087
(1.00) 		0.00183
(1.00)
Del Peak 40(18q22 1) 0 (0%) 153 0.268
(1.00) 		0.176
(1.00) 		0.125
(1.00) 		5.12e-10
(3.47e-07) 		0.299
(1.00) 		0.00582
(1.00) 		0.00562
(1.00) 		0.239
(1.00) 		0.0265
(1.00) 		0.000465
(0.305)
Amp Peak 1(2q33 1) 0 (0%) 334 0.0392
(1.00) 		0.358
(1.00) 		0.26
(1.00) 		0.267
(1.00) 		0.472
(1.00) 		0.634
(1.00) 		0.00341
(1.00) 		0.0898
(1.00) 		0.0758
(1.00) 		0.183
(1.00)
Amp Peak 2(5p13 2) 0 (0%) 332 0.342
(1.00) 		0.234
(1.00) 		0.321
(1.00) 		0.856
(1.00) 		1
(1.00) 		0.722
(1.00) 		0.0533
(1.00) 		0.211
(1.00) 		0.0458
(1.00) 		0.0846
(1.00)
Amp Peak 3(5q22 3) 0 (0%) 373 0.977
(1.00) 		0.768
(1.00) 		0.739
(1.00) 		0.333
(1.00) 		0.264
(1.00) 		0.00918
(1.00) 		0.217
(1.00) 		0.0912
(1.00) 		0.266
(1.00) 		0.331
(1.00)
Amp Peak 4(6p21 1) 0 (0%) 324 0.868
(1.00) 		0.829
(1.00) 		0.337
(1.00) 		0.0506
(1.00) 		0.00974
(1.00) 		0.605
(1.00) 		0.0194
(1.00) 		0.587
(1.00) 		0.013
(1.00) 		0.0459
(1.00)
Amp Peak 5(8p11 23) 0 (0%) 269 0.883
(1.00) 		0.293
(1.00) 		0.837
(1.00) 		0.168
(1.00) 		0.279
(1.00) 		0.577
(1.00) 		0.452
(1.00) 		0.821
(1.00) 		0.856
(1.00) 		0.423
(1.00)
Amp Peak 6(8p11 21) 0 (0%) 240 0.431
(1.00) 		0.449
(1.00) 		0.23
(1.00) 		0.184
(1.00) 		0.574
(1.00) 		0.475
(1.00) 		0.38
(1.00) 		0.32
(1.00) 		0.867
(1.00) 		0.712
(1.00)
Amp Peak 7(8q12 1) 0 (0%) 198 0.867
(1.00) 		0.113
(1.00) 		0.767
(1.00) 		0.0191
(1.00) 		0.249
(1.00) 		0.164
(1.00) 		0.434
(1.00) 		0.461
(1.00) 		0.0598
(1.00) 		0.629
(1.00)
Amp Peak 8(8q24 21) 0 (0%) 174 0.625
(1.00) 		0.074
(1.00) 		0.426
(1.00) 		0.0759
(1.00) 		0.267
(1.00) 		0.0879
(1.00) 		0.792
(1.00) 		0.382
(1.00) 		0.0494
(1.00) 		0.285
(1.00)
Amp Peak 9(11p15 5) 0 (0%) 327 0.592
(1.00) 		0.0407
(1.00) 		0.469
(1.00) 		0.00195
(1.00) 		0.111
(1.00) 		0.251
(1.00) 		0.244
(1.00) 		0.509
(1.00) 		0.265
(1.00) 		0.849
(1.00)
Amp Peak 10(12p13 33) 0 (0%) 309 0.19
(1.00) 		0.139
(1.00) 		0.82
(1.00) 		0.407
(1.00) 		0.575
(1.00) 		0.198
(1.00) 		0.501
(1.00) 		0.461
(1.00) 		0.829
(1.00) 		0.213
(1.00)
Amp Peak 15(17q12) 0 (0%) 312 0.488
(1.00) 		0.45
(1.00) 		0.302
(1.00) 		0.313
(1.00) 		0.57
(1.00) 		0.0121
(1.00) 		0.0115
(1.00) 		0.305
(1.00) 		0.144
(1.00) 		0.0815
(1.00)
Amp Peak 16(17q24 1) 0 (0%) 321 0.0711
(1.00) 		0.414
(1.00) 		0.636
(1.00) 		0.112
(1.00) 		0.531
(1.00) 		0.034
(1.00) 		0.0236
(1.00) 		0.498
(1.00) 		0.961
(1.00) 		0.315
(1.00)
Amp Peak 17(19p13 2) 0 (0%) 348 0.632
(1.00) 		0.618
(1.00) 		0.058
(1.00) 		0.228
(1.00) 		0.403
(1.00) 		0.00653
(1.00) 		0.279
(1.00) 		0.0853
(1.00) 		0.354
(1.00) 		0.52
(1.00)
Amp Peak 18(19q13 11) 0 (0%) 330 0.193
(1.00) 		0.68
(1.00) 		0.0658
(1.00) 		0.364
(1.00) 		0.491
(1.00) 		0.0219
(1.00) 		0.238
(1.00) 		0.592
(1.00) 		0.966
(1.00) 		0.588
(1.00)
Amp Peak 19(20p12 3) 0 (0%) 229 0.0503
(1.00) 		0.491
(1.00) 		0.199
(1.00) 		0.0553
(1.00) 		0.0876
(1.00) 		0.00408
(1.00) 		0.27
(1.00) 		0.0364
(1.00) 		0.0123
(1.00) 		0.001
(0.651)
Amp Peak 20(20p11 23) 0 (0%) 208 0.24
(1.00) 		0.974
(1.00) 		0.237
(1.00) 		0.0126
(1.00) 		0.121
(1.00) 		0.00224
(1.00) 		0.215
(1.00) 		0.0364
(1.00) 		0.124
(1.00) 		0.00187
(1.00)
Amp Peak 21(20p11 21) 0 (0%) 183 0.457
(1.00) 		0.466
(1.00) 		0.197
(1.00) 		0.00491
(1.00) 		0.258
(1.00) 		0.00326
(1.00) 		0.694
(1.00) 		0.0726
(1.00) 		0.323
(1.00) 		0.00639
(1.00)
Del Peak 2(1p33) 0 (0%) 306 0.00145
(0.93) 		0.89
(1.00) 		0.911
(1.00) 		0.0987
(1.00) 		0.572
(1.00) 		0.00752
(1.00) 		0.0208
(1.00) 		0.266
(1.00) 		0.0145
(1.00) 		0.0148
(1.00)
Del Peak 3(1p13 1) 0 (0%) 310 0.0566
(1.00) 		0.891
(1.00) 		0.569
(1.00) 		0.177
(1.00) 		1
(1.00) 		0.000757
(0.493) 		0.00324
(1.00) 		0.0622
(1.00) 		0.00935
(1.00) 		0.00587
(1.00)
Del Peak 4(1q43) 0 (0%) 369 0.476
(1.00) 		0.525
(1.00) 		1
(1.00) 		1
(1.00) 		0.287
(1.00) 		0.0752
(1.00) 		0.454
(1.00) 		0.254
(1.00) 		0.291
(1.00) 		0.135
(1.00)
Del Peak 5(2q37 2) 0 (0%) 392 0.372
(1.00) 		0.447
(1.00) 		0.372
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.364
(1.00) 		0.963
(1.00) 		0.233
(1.00) 		0.168
(1.00) 		0.879
(1.00)
Del Peak 6(3p26 1) 0 (0%) 353 0.000441
(0.29) 		0.346
(1.00) 		1
(1.00) 		0.146
(1.00) 		1
(1.00) 		0.000436
(0.287) 		0.00221
(1.00) 		0.0883
(1.00) 		0.177
(1.00) 		0.00742
(1.00)
Del Peak 7(3p14 2) 0 (0%) 338 0.468
(1.00) 		0.608
(1.00) 		0.308
(1.00) 		0.186
(1.00) 		1
(1.00) 		0.0556
(1.00) 		0.277
(1.00) 		0.36
(1.00) 		0.0322
(1.00) 		0.179
(1.00)
Del Peak 8(3q26 31) 0 (0%) 374 0.453
(1.00) 		0.85
(1.00) 		1
(1.00) 		0.14
(1.00) 		1
(1.00) 		0.62
(1.00) 		0.321
(1.00) 		0.674
(1.00) 		0.374
(1.00) 		0.0581
(1.00)
Del Peak 10(4q22 1) 0 (0%) 287 0.0103
(1.00) 		0.967
(1.00) 		0.594
(1.00) 		0.0176
(1.00) 		0.0279
(1.00) 		0.114
(1.00) 		0.0242
(1.00) 		0.85
(1.00) 		0.0153
(1.00) 		0.0106
(1.00)
Del Peak 11(4q35 1) 0 (0%) 276 0.0476
(1.00) 		0.255
(1.00) 		0.209
(1.00) 		0.0871
(1.00) 		0.036
(1.00) 		0.215
(1.00) 		0.132
(1.00) 		0.315
(1.00) 		0.0635
(1.00) 		0.168
(1.00)
Del Peak 12(5q11 2) 0 (0%) 322 0.0469
(1.00) 		0.0453
(1.00) 		0.342
(1.00) 		0.112
(1.00) 		0.124
(1.00) 		0.0556
(1.00) 		0.046
(1.00) 		0.615
(1.00) 		0.0149
(1.00) 		0.0132
(1.00)
Del Peak 13(5q21 3) 0 (0%) 296 0.0709
(1.00) 		0.0679
(1.00) 		0.662
(1.00) 		0.196
(1.00) 		0.0223
(1.00) 		0.0193
(1.00) 		0.0017
(1.00) 		0.237
(1.00) 		0.00516
(1.00) 		0.00139
(0.893)
Del Peak 14(5q23 1) 0 (0%) 306 0.125
(1.00) 		0.285
(1.00) 		0.216
(1.00) 		0.0987
(1.00) 		0.017
(1.00) 		0.0111
(1.00) 		0.0323
(1.00) 		0.3
(1.00) 		0.0287
(1.00) 		0.0701
(1.00)
Del Peak 15(6p25 3) 0 (0%) 359 0.696
(1.00) 		0.0948
(1.00) 		0.0804
(1.00) 		0.516
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.501
(1.00) 		0.285
(1.00) 		0.738
(1.00) 		0.663
(1.00)
Del Peak 16(6q26) 0 (0%) 353 0.0202
(1.00) 		0.928
(1.00) 		0.889
(1.00) 		1
(1.00) 		1
(1.00) 		0.0205
(1.00) 		0.0376
(1.00) 		0.0621
(1.00) 		0.0144
(1.00) 		0.0695
(1.00)
Del Peak 17(7q31 1) 0 (0%) 402 0.875
(1.00) 		0.589
(1.00) 		0.36
(1.00) 		1
(1.00) 		1
(1.00) 		0.5
(1.00) 		0.731
(1.00) 		1
(1.00) 		0.666
(1.00) 		0.943
(1.00)
Del Peak 18(8p23 3) 0 (0%) 242 0.552
(1.00) 		0.251
(1.00) 		0.161
(1.00) 		0.0748
(1.00) 		0.572
(1.00) 		0.0213
(1.00) 		0.00104
(0.677) 		0.0863
(1.00) 		0.00532
(1.00) 		0.0122
(1.00)
Del Peak 20(8p11 22) 0 (0%) 333 0.407
(1.00) 		0.236
(1.00) 		0.804
(1.00) 		0.461
(1.00) 		0.0973
(1.00) 		0.0865
(1.00) 		0.00891
(1.00) 		0.252
(1.00) 		0.0333
(1.00) 		0.0236
(1.00)
Del Peak 21(8p11 21) 0 (0%) 370 0.833
(1.00) 		0.377
(1.00) 		1
(1.00) 		0.632
(1.00) 		0.282
(1.00) 		0.0077
(1.00) 		0.00107
(0.69) 		0.129
(1.00) 		0.0181
(1.00) 		0.00206
(1.00)
Del Peak 22(9p21 3) 0 (0%) 357 0.0222
(1.00) 		0.0603
(1.00) 		0.253
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.104
(1.00) 		0.0291
(1.00) 		0.636
(1.00) 		0.309
(1.00) 		0.483
(1.00)
Del Peak 23(10p15 3) 0 (0%) 345 0.883
(1.00) 		0.434
(1.00) 		0.79
(1.00) 		0.557
(1.00) 		0.0717
(1.00) 		0.00222
(1.00) 		0.0139
(1.00) 		0.605
(1.00) 		0.0712
(1.00) 		0.00112
(0.723)
Del Peak 24(10q21 1) 0 (0%) 331 0.993
(1.00) 		0.0528
(1.00) 		0.387
(1.00) 		0.0995
(1.00) 		0.102
(1.00) 		0.0955
(1.00) 		0.0174
(1.00) 		0.0445
(1.00) 		0.0801
(1.00) 		0.00276
(1.00)
Del Peak 25(10q23 31) 0 (0%) 319 0.803
(1.00) 		0.0124
(1.00) 		0.481
(1.00) 		0.164
(1.00) 		0.131
(1.00) 		0.00788
(1.00) 		0.0272
(1.00) 		0.142
(1.00) 		0.0907
(1.00) 		0.00308
(1.00)
Del Peak 26(10q25 2) 0 (0%) 320 0.342
(1.00) 		0.164
(1.00) 		0.906
(1.00) 		0.164
(1.00) 		0.129
(1.00) 		0.0665
(1.00) 		0.0211
(1.00) 		0.0467
(1.00) 		0.0781
(1.00) 		0.0368
(1.00)
Del Peak 27(12p13 2) 0 (0%) 369 0.385
(1.00) 		0.633
(1.00) 		0.268
(1.00) 		0.00324
(1.00) 		1
(1.00) 		0.163
(1.00) 		0.203
(1.00) 		0.702
(1.00) 		0.697
(1.00) 		0.211
(1.00)
Del Peak 29(14q32 11) 0 (0%) 280 0.375
(1.00) 		0.506
(1.00) 		0.752
(1.00) 		0.000929
(0.605) 		0.554
(1.00) 		0.0356
(1.00) 		0.154
(1.00) 		0.26
(1.00) 		0.136
(1.00) 		0.156
(1.00)
Del Peak 30(15q11 2) 0 (0%) 253 0.912
(1.00) 		0.852
(1.00) 		0.92
(1.00) 		0.0238
(1.00) 		0.0575
(1.00) 		0.061
(1.00) 		0.17
(1.00) 		0.601
(1.00) 		0.252
(1.00) 		0.0418
(1.00)
Del Peak 31(15q21 1) 0 (0%) 262 0.0892
(1.00) 		0.658
(1.00) 		1
(1.00) 		0.0485
(1.00) 		0.0483
(1.00) 		0.085
(1.00) 		0.281
(1.00) 		0.378
(1.00) 		0.467
(1.00) 		0.34
(1.00)
Del Peak 32(15q22 33) 0 (0%) 268 0.245
(1.00) 		0.426
(1.00) 		1
(1.00) 		0.00861
(1.00) 		0.0427
(1.00) 		0.0456
(1.00) 		0.318
(1.00) 		0.878
(1.00) 		0.33
(1.00) 		0.08
(1.00)
Del Peak 33(16p13 3) 0 (0%) 368 0.00274
(1.00) 		0.426
(1.00) 		0.874
(1.00) 		1
(1.00) 		1
(1.00) 		0.355
(1.00) 		0.109
(1.00) 		0.781
(1.00) 		0.109
(1.00) 		0.0846
(1.00)
Del Peak 34(16q23 1) 0 (0%) 364 0.00121
(0.779) 		0.288
(1.00) 		0.128
(1.00) 		0.26
(1.00) 		1
(1.00) 		0.979
(1.00) 		0.358
(1.00) 		0.898
(1.00) 		0.26
(1.00) 		0.896
(1.00)
Del Peak 36(17q24 3) 0 (0%) 354 0.721
(1.00) 		0.51
(1.00) 		0.398
(1.00) 		0.838
(1.00) 		1
(1.00) 		0.249
(1.00) 		0.00503
(1.00) 		0.231
(1.00) 		0.0379
(1.00) 		0.0619
(1.00)
Del Peak 41(19p13 3) 0 (0%) 356 0.37
(1.00) 		0.148
(1.00) 		0.775
(1.00) 		0.202
(1.00) 		0.36
(1.00) 		0.0313
(1.00) 		0.000667
(0.436) 		0.0848
(1.00) 		0.00169
(1.00) 		0.000633
(0.414)
Del Peak 42(20p12 1) 0 (0%) 334 0.804
(1.00) 		0.439
(1.00) 		0.617
(1.00) 		0.137
(1.00) 		1
(1.00) 		0.983
(1.00) 		0.85
(1.00) 		0.782
(1.00) 		0.531
(1.00) 		0.495
(1.00)
Del Peak 43(21q11 2) 0 (0%) 288 0.489
(1.00) 		0.722
(1.00) 		0.831
(1.00) 		0.0101
(1.00) 		0.219
(1.00) 		0.336
(1.00) 		0.282
(1.00) 		0.796
(1.00) 		0.0108
(1.00) 		0.435
(1.00)
Del Peak 44(22q13 32) 0 (0%) 275 0.222
(1.00) 		0.701
(1.00) 		0.754
(1.00) 		0.005
(1.00) 		1
(1.00) 		0.0337
(1.00) 		0.00451
(1.00) 		0.515
(1.00) 		0.00975
(1.00) 		0.0175
(1.00)
'Amp Peak 11(13q12.13)' versus 'HISTOLOGICAL.TYPE'

P value = 9.63e-07 (Fisher's exact test), Q value = 0.00065

Table S1.  Gene #11: 'Amp Peak 11(13q12.13)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
AMP PEAK 11(13Q12.13) CNV 233 16
AMP PEAK 11(13Q12.13) WILD-TYPE 124 38

Figure S1.  Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 12(13q22.1)' versus 'HISTOLOGICAL.TYPE'

P value = 8.61e-06 (Fisher's exact test), Q value = 0.0058

Table S2.  Gene #12: 'Amp Peak 12(13q22.1)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
AMP PEAK 12(13Q22.1) CNV 235 18
AMP PEAK 12(13Q22.1) WILD-TYPE 122 36

Figure S2.  Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 13(16p11.2)' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00036 (Chi-square test), Q value = 0.24

Table S3.  Gene #13: 'Amp Peak 13(16p11.2)' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 68 1 33 116 8 1 22 13 47 34 40 16 1
AMP PEAK 13(16P11.2) CNV 11 1 4 26 1 0 5 9 19 15 14 4 0
AMP PEAK 13(16P11.2) WILD-TYPE 57 0 29 90 7 1 17 4 28 19 26 12 1

Figure S3.  Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

'Amp Peak 14(16q12.1)' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.95e-05 (Chi-square test), Q value = 0.06

Table S4.  Gene #14: 'Amp Peak 14(16q12.1)' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 68 1 33 116 8 1 22 13 47 34 40 16 1
AMP PEAK 14(16Q12.1) CNV 11 1 3 20 1 0 5 9 19 13 11 3 0
AMP PEAK 14(16Q12.1) WILD-TYPE 57 0 30 96 7 1 17 4 28 21 29 13 1

Figure S4.  Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

'Amp Peak 22(20q11.21)' versus 'HISTOLOGICAL.TYPE'

P value = 7.35e-06 (Fisher's exact test), Q value = 0.0049

Table S5.  Gene #22: 'Amp Peak 22(20q11.21)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
AMP PEAK 22(20Q11.21) CNV 270 24
AMP PEAK 22(20Q11.21) WILD-TYPE 87 30

Figure S5.  Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 23(20q12)' versus 'HISTOLOGICAL.TYPE'

P value = 1.31e-06 (Fisher's exact test), Q value = 0.00088

Table S6.  Gene #23: 'Amp Peak 23(20q12)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
AMP PEAK 23(20Q12) CNV 272 23
AMP PEAK 23(20Q12) WILD-TYPE 85 31

Figure S6.  Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 24(20q13.32)' versus 'HISTOLOGICAL.TYPE'

P value = 4.75e-06 (Fisher's exact test), Q value = 0.0032

Table S7.  Gene #24: 'Amp Peak 24(20q13.32)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
AMP PEAK 24(20Q13.32) CNV 274 24
AMP PEAK 24(20Q13.32) WILD-TYPE 83 30

Figure S7.  Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 1(1p36.11)' versus 'DISTANT.METASTASIS'

P value = 0.000113 (Chi-square test), Q value = 0.075

Table S8.  Gene #25: 'Del Peak 1(1p36.11)' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 313 49 7 1 36
DEL PEAK 1(1P36.11) CNV 101 33 2 0 13
DEL PEAK 1(1P36.11) WILD-TYPE 212 16 5 1 23

Figure S8.  Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Clinical Feature #6: 'DISTANT.METASTASIS'

'Del Peak 9(4p16.2)' versus 'Time to Death'

P value = 0.000312 (logrank test), Q value = 0.21

Table S9.  Gene #33: 'Del Peak 9(4p16.2)' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 321 49 0.1 - 135.5 (7.7)
DEL PEAK 9(4P16.2) CNV 91 20 0.2 - 87.8 (7.6)
DEL PEAK 9(4P16.2) WILD-TYPE 230 29 0.1 - 135.5 (8.0)

Figure S9.  Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 9(4p16.2)' versus 'DISTANT.METASTASIS'

P value = 0.000248 (Chi-square test), Q value = 0.16

Table S10.  Gene #33: 'Del Peak 9(4p16.2)' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 313 49 7 1 36
DEL PEAK 9(4P16.2) CNV 75 27 3 0 12
DEL PEAK 9(4P16.2) WILD-TYPE 238 22 4 1 24

Figure S10.  Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Clinical Feature #6: 'DISTANT.METASTASIS'

'Del Peak 19(8p22)' versus 'LYMPH.NODE.METASTASIS'

P value = 7.07e-05 (Chi-square test), Q value = 0.047

Table S11.  Gene #43: 'Del Peak 19(8p22)' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 244 69 13 12 2 58 4 9 1
DEL PEAK 19(8P22) CNV 86 38 8 3 1 40 1 6 1
DEL PEAK 19(8P22) WILD-TYPE 158 31 5 9 1 18 3 3 0

Figure S11.  Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

'Del Peak 19(8p22)' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000229 (Chi-square test), Q value = 0.15

Table S12.  Gene #43: 'Del Peak 19(8p22)' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 68 1 33 116 8 1 22 13 47 34 40 16 1
DEL PEAK 19(8P22) CNV 24 0 9 41 2 0 11 8 24 23 26 12 1
DEL PEAK 19(8P22) WILD-TYPE 44 1 24 75 6 1 11 5 23 11 14 4 0

Figure S12.  Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

'Del Peak 28(13q14.13)' versus 'DISTANT.METASTASIS'

P value = 4.21e-05 (Chi-square test), Q value = 0.028

Table S13.  Gene #52: 'Del Peak 28(13q14.13)' versus Clinical Feature #6: 'DISTANT.METASTASIS'

nPatients M0 M1 M1A M1B MX
ALL 313 49 7 1 36
DEL PEAK 28(13Q14.13) CNV 12 1 0 1 2
DEL PEAK 28(13Q14.13) WILD-TYPE 301 48 7 0 34

Figure S13.  Get High-res Image Gene #52: 'Del Peak 28(13q14.13)' versus Clinical Feature #6: 'DISTANT.METASTASIS'

'Del Peak 35(17p12)' versus 'HISTOLOGICAL.TYPE'

P value = 3.61e-06 (Fisher's exact test), Q value = 0.0024

Table S14.  Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
DEL PEAK 35(17P12) CNV 213 14
DEL PEAK 35(17P12) WILD-TYPE 144 40

Figure S14.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 35(17p12)' versus 'LYMPH.NODE.METASTASIS'

P value = 0.000291 (Chi-square test), Q value = 0.19

Table S15.  Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 244 69 13 12 2 58 4 9 1
DEL PEAK 35(17P12) CNV 112 48 6 9 1 43 1 7 1
DEL PEAK 35(17P12) WILD-TYPE 132 21 7 3 1 15 3 2 0

Figure S15.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #7: 'LYMPH.NODE.METASTASIS'

'Del Peak 35(17p12)' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.46e-05 (t-test), Q value = 0.043

Table S16.  Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 389 2.0 (4.5)
DEL PEAK 35(17P12) CNV 216 2.8 (5.5)
DEL PEAK 35(17P12) WILD-TYPE 173 1.1 (2.4)

Figure S16.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #9: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 35(17p12)' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.8e-05 (Chi-square test), Q value = 0.032

Table S17.  Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 68 1 33 116 8 1 22 13 47 34 40 16 1
DEL PEAK 35(17P12) CNV 33 0 15 49 1 1 13 12 29 26 30 11 1
DEL PEAK 35(17P12) WILD-TYPE 35 1 18 67 7 0 9 1 18 8 10 5 0

Figure S17.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

'Del Peak 37(18p11.31)' versus 'HISTOLOGICAL.TYPE'

P value = 8.95e-11 (Fisher's exact test), Q value = 6.1e-08

Table S18.  Gene #61: 'Del Peak 37(18p11.31)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
DEL PEAK 37(18P11.31) CNV 211 7
DEL PEAK 37(18P11.31) WILD-TYPE 146 47

Figure S18.  Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 38(18q12.2)' versus 'HISTOLOGICAL.TYPE'

P value = 3.31e-10 (Fisher's exact test), Q value = 2.2e-07

Table S19.  Gene #62: 'Del Peak 38(18q12.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
DEL PEAK 38(18Q12.2) CNV 235 11
DEL PEAK 38(18Q12.2) WILD-TYPE 122 43

Figure S19.  Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 39(18q21.2)' versus 'HISTOLOGICAL.TYPE'

P value = 4.16e-09 (Fisher's exact test), Q value = 2.8e-06

Table S20.  Gene #63: 'Del Peak 39(18q21.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
DEL PEAK 39(18Q21.2) CNV 245 14
DEL PEAK 39(18Q21.2) WILD-TYPE 112 40

Figure S20.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 39(18q21.2)' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000167 (Chi-square test), Q value = 0.11

Table S21.  Gene #63: 'Del Peak 39(18q21.2)' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 68 1 33 116 8 1 22 13 47 34 40 16 1
DEL PEAK 39(18Q21.2) CNV 36 0 18 62 2 1 12 12 31 28 34 13 1
DEL PEAK 39(18Q21.2) WILD-TYPE 32 1 15 54 6 0 10 1 16 6 6 3 0

Figure S21.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Clinical Feature #11: 'NEOPLASM.DISEASESTAGE'

'Del Peak 40(18q22.1)' versus 'HISTOLOGICAL.TYPE'

P value = 5.12e-10 (Fisher's exact test), Q value = 3.5e-07

Table S22.  Gene #64: 'Del Peak 40(18q22.1)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 357 54
DEL PEAK 40(18Q22.1) CNV 246 13
DEL PEAK 40(18Q22.1) WILD-TYPE 111 41

Figure S22.  Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

  • Mutation data file = all_lesions.conf_99.cnv.cluster.txt

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

  • Number of patients = 413

  • Number of significantly arm-level cnvs = 68

  • 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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