Correlation between copy number variation genes (focal) and selected clinical features
Colon/Rectal Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
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/C15D8PV8
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 75 arm-level results and 12 clinical features across 575 patients, 35 significant findings detected with Q value < 0.25.

  • Amp Peak 2(2q33.1) cnv correlated to 'LYMPH.NODE.METASTASIS'.

  • Amp Peak 6(7p21.3) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 11(10q22.3) cnv correlated to 'LYMPH.NODE.METASTASIS'.

  • Amp Peak 14(13q12.13) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 15(13q12.2) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 16(13q22.1) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 24(20p11.21) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 25(20q11.21) cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • Amp Peak 26(20q12) cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'HISTOLOGICAL.TYPE', and 'NEOPLASM.DISEASESTAGE'.

  • Amp Peak 27(20q13.32) cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • Del Peak 10(4p16.1) cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

  • Del Peak 18(8p23.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'HISTOLOGICAL.TYPE', and 'LYMPH.NODE.METASTASIS'.

  • Del Peak 19(8p22) cnv correlated to 'HISTOLOGICAL.TYPE',  'LYMPH.NODE.METASTASIS', and 'NUMBER.OF.LYMPH.NODES'.

  • Del Peak 30(14q22.1) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 34(16p13.3) cnv correlated to 'Time to Death'.

  • Del Peak 36(17p12) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 38(18p11.31) cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • Del Peak 39(18q12.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • Del Peak 40(18q21.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'HISTOLOGICAL.TYPE',  'LYMPH.NODE.METASTASIS', and 'NEOPLASM.DISEASESTAGE'.

  • Del Peak 41(18q22.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'HISTOLOGICAL.TYPE', and 'NEOPLASM.DISEASESTAGE'.

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 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 35 significant findings detected.

Clinical
Features
Time
to
Death
AGE PRIMARY
SITE
OF
DISEASE
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 Chi-square test Fisher's exact test t-test t-test Chi-square test
Del Peak 40(18q21 2) 0 (0%) 172 0.493
(1.00)
0.0823
(1.00)
1.07e-09
(8.75e-07)
0.144
(1.00)
3.54e-16
(2.92e-13)
0.0637
(1.00)
0.0015
(1.00)
0.000227
(0.18)
0.0558
(1.00)
0.00113
(0.864)
4.49e-05
(0.0359)
Amp Peak 26(20q12) 0 (0%) 134 0.268
(1.00)
0.726
(1.00)
4.74e-06
(0.00383)
0.325
(1.00)
5.41e-13
(4.44e-10)
0.692
(1.00)
0.00133
(1.00)
0.0446
(1.00)
0.0683
(1.00)
0.385
(1.00)
0.00019
(0.151)
Del Peak 18(8p23 2) 0 (0%) 303 0.606
(1.00)
0.205
(1.00)
2.4e-05
(0.0193)
0.155
(1.00)
2.72e-05
(0.0219)
0.0155
(1.00)
0.00935
(1.00)
0.000164
(0.13)
0.00768
(1.00)
0.000456
(0.358)
0.00132
(1.00)
Del Peak 19(8p22) 0 (0%) 290 0.581
(1.00)
0.317
(1.00)
0.000379
(0.299)
0.358
(1.00)
0.000245
(0.194)
0.0196
(1.00)
0.00357
(1.00)
1.79e-05
(0.0144)
0.0104
(1.00)
0.000114
(0.0912)
0.00037
(0.292)
Del Peak 41(18q22 1) 0 (0%) 177 0.343
(1.00)
0.221
(1.00)
1.94e-07
(0.000158)
0.206
(1.00)
2.05e-15
(1.68e-12)
0.0632
(1.00)
0.00221
(1.00)
0.00177
(1.00)
0.108
(1.00)
0.00209
(1.00)
0.000104
(0.0831)
Amp Peak 25(20q11 21) 0 (0%) 136 0.31
(1.00)
0.823
(1.00)
9.13e-06
(0.00737)
0.327
(1.00)
7.95e-12
(6.52e-09)
0.693
(1.00)
0.00547
(1.00)
0.0526
(1.00)
0.0685
(1.00)
0.337
(1.00)
0.000699
(0.541)
Amp Peak 27(20q13 32) 0 (0%) 131 0.361
(1.00)
0.658
(1.00)
2.18e-05
(0.0175)
0.55
(1.00)
8.79e-12
(7.2e-09)
0.692
(1.00)
0.00436
(1.00)
0.0501
(1.00)
0.0671
(1.00)
0.24
(1.00)
0.000657
(0.509)
Del Peak 38(18p11 31) 0 (0%) 234 0.976
(1.00)
0.059
(1.00)
1.82e-06
(0.00148)
0.932
(1.00)
1.52e-16
(1.25e-13)
0.322
(1.00)
0.000547
(0.429)
0.138
(1.00)
0.0199
(1.00)
0.487
(1.00)
0.00232
(1.00)
Del Peak 39(18q12 2) 0 (0%) 189 0.923
(1.00)
0.0817
(1.00)
1.57e-09
(1.28e-06)
0.424
(1.00)
8.26e-18
(6.82e-15)
0.034
(1.00)
0.00422
(1.00)
0.00484
(1.00)
0.056
(1.00)
0.00963
(1.00)
0.000584
(0.456)
Amp Peak 2(2q33 1) 0 (0%) 452 0.129
(1.00)
0.385
(1.00)
0.031
(1.00)
1
(1.00)
0.00372
(1.00)
0.103
(1.00)
0.535
(1.00)
0.000238
(0.188)
0.397
(1.00)
0.0257
(1.00)
0.0255
(1.00)
Amp Peak 6(7p21 3) 0 (0%) 238 0.294
(1.00)
0.103
(1.00)
0.0292
(1.00)
0.671
(1.00)
0.000225
(0.179)
0.0882
(1.00)
0.0259
(1.00)
0.000569
(0.445)
0.148
(1.00)
0.0314
(1.00)
0.000392
(0.308)
Amp Peak 11(10q22 3) 0 (0%) 540 0.819
(1.00)
0.303
(1.00)
1
(1.00)
0.488
(1.00)
0.931
(1.00)
0.434
(1.00)
0.911
(1.00)
2.77e-05
(0.0222)
0.919
(1.00)
0.087
(1.00)
0.464
(1.00)
Amp Peak 14(13q12 13) 0 (0%) 204 0.122
(1.00)
0.314
(1.00)
0.00246
(1.00)
0.663
(1.00)
1.21e-09
(9.85e-07)
1
(1.00)
0.0104
(1.00)
0.00114
(0.868)
0.0545
(1.00)
0.031
(1.00)
0.000587
(0.458)
Amp Peak 15(13q12 2) 0 (0%) 209 0.0977
(1.00)
0.239
(1.00)
0.00188
(1.00)
0.487
(1.00)
2.65e-09
(2.16e-06)
1
(1.00)
0.0238
(1.00)
0.00237
(1.00)
0.0962
(1.00)
0.0323
(1.00)
0.00161
(1.00)
Amp Peak 16(13q22 1) 0 (0%) 204 0.0436
(1.00)
0.444
(1.00)
0.0249
(1.00)
0.191
(1.00)
3.25e-08
(2.65e-05)
0.503
(1.00)
0.0248
(1.00)
0.000608
(0.474)
0.284
(1.00)
0.172
(1.00)
0.0118
(1.00)
Amp Peak 24(20p11 21) 0 (0%) 236 0.806
(1.00)
0.709
(1.00)
0.00784
(1.00)
0.0505
(1.00)
1.14e-05
(0.00919)
0.32
(1.00)
0.00329
(1.00)
0.691
(1.00)
0.68
(1.00)
0.923
(1.00)
0.0374
(1.00)
Del Peak 10(4p16 1) 0 (0%) 393 0.0429
(1.00)
0.954
(1.00)
0.0561
(1.00)
0.106
(1.00)
0.0275
(1.00)
2.78e-05
(0.0222)
0.0125
(1.00)
0.00495
(1.00)
0.0508
(1.00)
0.00162
(1.00)
0.00639
(1.00)
Del Peak 30(14q22 1) 0 (0%) 390 0.211
(1.00)
0.233
(1.00)
0.0212
(1.00)
0.422
(1.00)
1.15e-06
(0.00093)
0.725
(1.00)
0.143
(1.00)
0.0171
(1.00)
0.856
(1.00)
0.693
(1.00)
0.552
(1.00)
Del Peak 34(16p13 3) 0 (0%) 517 8.33e-05
(0.0666)
0.254
(1.00)
0.359
(1.00)
0.89
(1.00)
0.421
(1.00)
0.609
(1.00)
0.38
(1.00)
0.179
(1.00)
0.797
(1.00)
0.059
(1.00)
0.0498
(1.00)
Del Peak 36(17p12) 0 (0%) 232 0.674
(1.00)
0.0983
(1.00)
0.00169
(1.00)
0.551
(1.00)
6.55e-08
(5.33e-05)
0.325
(1.00)
0.0397
(1.00)
0.000609
(0.474)
0.261
(1.00)
0.00263
(1.00)
0.00229
(1.00)
Amp Peak 1(1q31 1) 0 (0%) 441 0.454
(1.00)
0.292
(1.00)
0.0268
(1.00)
0.198
(1.00)
0.0927
(1.00)
0.0357
(1.00)
0.171
(1.00)
0.0195
(1.00)
0.632
(1.00)
0.0141
(1.00)
0.327
(1.00)
Amp Peak 3(5p12) 0 (0%) 468 0.015
(1.00)
0.372
(1.00)
0.151
(1.00)
0.83
(1.00)
0.056
(1.00)
0.379
(1.00)
0.349
(1.00)
0.113
(1.00)
0.037
(1.00)
0.0665
(1.00)
0.164
(1.00)
Amp Peak 4(5q22 3) 0 (0%) 516 0.757
(1.00)
0.865
(1.00)
0.445
(1.00)
0.891
(1.00)
0.315
(1.00)
1
(1.00)
0.0314
(1.00)
0.23
(1.00)
0.0768
(1.00)
0.476
(1.00)
0.505
(1.00)
Amp Peak 5(6p21 1) 0 (0%) 429 0.476
(1.00)
0.682
(1.00)
0.0314
(1.00)
0.151
(1.00)
0.00234
(1.00)
0.00136
(1.00)
0.106
(1.00)
0.000788
(0.608)
0.176
(1.00)
0.0025
(1.00)
0.0197
(1.00)
Amp Peak 7(8p11 23) 0 (0%) 379 0.458
(1.00)
0.752
(1.00)
0.625
(1.00)
0.428
(1.00)
0.238
(1.00)
0.498
(1.00)
0.426
(1.00)
0.456
(1.00)
0.169
(1.00)
0.634
(1.00)
0.172
(1.00)
Amp Peak 8(8p11 21) 0 (0%) 337 0.653
(1.00)
0.597
(1.00)
0.636
(1.00)
0.175
(1.00)
0.122
(1.00)
0.742
(1.00)
0.316
(1.00)
0.301
(1.00)
0.047
(1.00)
0.429
(1.00)
0.126
(1.00)
Amp Peak 9(8q12 1) 0 (0%) 266 0.92
(1.00)
0.19
(1.00)
0.303
(1.00)
0.557
(1.00)
0.0095
(1.00)
0.0423
(1.00)
0.027
(1.00)
0.171
(1.00)
0.107
(1.00)
0.0282
(1.00)
0.0546
(1.00)
Amp Peak 10(8q24 21) 0 (0%) 230 0.531
(1.00)
0.236
(1.00)
0.0863
(1.00)
0.349
(1.00)
0.0112
(1.00)
0.0931
(1.00)
0.0571
(1.00)
0.569
(1.00)
0.215
(1.00)
0.0656
(1.00)
0.144
(1.00)
Amp Peak 12(11p15 5) 0 (0%) 446 0.711
(1.00)
0.0608
(1.00)
0.145
(1.00)
0.548
(1.00)
0.00145
(1.00)
0.12
(1.00)
0.383
(1.00)
0.809
(1.00)
0.878
(1.00)
0.429
(1.00)
0.99
(1.00)
Amp Peak 13(12p13 32) 0 (0%) 431 0.257
(1.00)
0.0696
(1.00)
0.829
(1.00)
0.501
(1.00)
0.336
(1.00)
0.698
(1.00)
0.0847
(1.00)
0.446
(1.00)
0.744
(1.00)
0.447
(1.00)
0.158
(1.00)
Amp Peak 17(15q26 1) 0 (0%) 532 0.0799
(1.00)
0.753
(1.00)
0.291
(1.00)
0.0573
(1.00)
0.429
(1.00)
0.141
(1.00)
0.649
(1.00)
0.0323
(1.00)
0.602
(1.00)
0.0547
(1.00)
0.124
(1.00)
Amp Peak 18(16p11 2) 0 (0%) 414 0.843
(1.00)
0.26
(1.00)
0.918
(1.00)
0.643
(1.00)
0.00247
(1.00)
0.715
(1.00)
0.108
(1.00)
0.00225
(1.00)
0.278
(1.00)
0.0162
(1.00)
0.000886
(0.682)
Amp Peak 19(17q12) 0 (0%) 431 0.492
(1.00)
0.363
(1.00)
0.591
(1.00)
0.102
(1.00)
0.456
(1.00)
0.462
(1.00)
0.0112
(1.00)
0.0123
(1.00)
0.0732
(1.00)
0.351
(1.00)
0.155
(1.00)
Amp Peak 20(17q24 1) 0 (0%) 447 0.0404
(1.00)
0.245
(1.00)
0.911
(1.00)
0.616
(1.00)
0.0884
(1.00)
0.691
(1.00)
0.0535
(1.00)
0.0443
(1.00)
0.232
(1.00)
0.711
(1.00)
0.483
(1.00)
Amp Peak 21(19p13 2) 0 (0%) 478 0.14
(1.00)
0.493
(1.00)
0.216
(1.00)
0.219
(1.00)
0.0514
(1.00)
1
(1.00)
0.23
(1.00)
0.219
(1.00)
0.119
(1.00)
0.994
(1.00)
0.578
(1.00)
Amp Peak 22(19q12) 0 (0%) 453 0.625
(1.00)
0.941
(1.00)
0.256
(1.00)
0.22
(1.00)
0.0292
(1.00)
0.692
(1.00)
0.135
(1.00)
0.583
(1.00)
0.474
(1.00)
0.403
(1.00)
0.785
(1.00)
Amp Peak 23(20p11 23) 0 (0%) 274 0.702
(1.00)
0.921
(1.00)
0.0194
(1.00)
0.0446
(1.00)
0.00073
(0.563)
0.181
(1.00)
0.00143
(1.00)
0.169
(1.00)
0.382
(1.00)
0.295
(1.00)
0.00642
(1.00)
Amp Peak 28(Xq28) 0 (0%) 454 0.252
(1.00)
0.209
(1.00)
0.421
(1.00)
0.758
(1.00)
0.0252
(1.00)
0.693
(1.00)
0.228
(1.00)
0.0168
(1.00)
0.358
(1.00)
0.271
(1.00)
0.0707
(1.00)
Del Peak 1(1p36 11) 0 (0%) 353 0.0525
(1.00)
0.105
(1.00)
0.126
(1.00)
0.345
(1.00)
0.0065
(1.00)
0.739
(1.00)
0.000579
(0.453)
0.0134
(1.00)
0.102
(1.00)
0.000524
(0.411)
0.0263
(1.00)
Del Peak 2(1p33) 0 (0%) 419 0.0185
(1.00)
0.836
(1.00)
0.401
(1.00)
0.851
(1.00)
0.079
(1.00)
0.709
(1.00)
0.0103
(1.00)
0.0233
(1.00)
0.314
(1.00)
0.0143
(1.00)
0.022
(1.00)
Del Peak 3(1p13 2) 0 (0%) 418 0.072
(1.00)
0.841
(1.00)
0.248
(1.00)
0.64
(1.00)
0.135
(1.00)
0.265
(1.00)
0.00123
(0.933)
0.00247
(1.00)
0.243
(1.00)
0.00268
(1.00)
0.00657
(1.00)
Del Peak 4(2p12) 0 (0%) 555 0.81
(1.00)
0.179
(1.00)
0.00346
(1.00)
0.821
(1.00)
0.0206
(1.00)
0.275
(1.00)
0.56
(1.00)
0.882
(1.00)
0.885
(1.00)
0.315
(1.00)
0.358
(1.00)
Del Peak 5(2q22 1) 0 (0%) 542 0.855
(1.00)
0.564
(1.00)
0.842
(1.00)
0.474
(1.00)
0.927
(1.00)
1
(1.00)
0.691
(1.00)
0.829
(1.00)
1
(1.00)
0.912
(1.00)
0.474
(1.00)
Del Peak 6(2q37 2) 0 (0%) 545 0.845
(1.00)
0.139
(1.00)
0.835
(1.00)
0.456
(1.00)
0.944
(1.00)
1
(1.00)
0.134
(1.00)
0.73
(1.00)
0.398
(1.00)
0.867
(1.00)
0.273
(1.00)
Del Peak 7(3p26 3) 0 (0%) 491 0.000649
(0.504)
0.855
(1.00)
0.691
(1.00)
0.723
(1.00)
0.193
(1.00)
0.131
(1.00)
0.00101
(0.778)
0.0172
(1.00)
0.0636
(1.00)
0.0284
(1.00)
0.00837
(1.00)
Del Peak 8(3p14 2) 0 (0%) 471 0.231
(1.00)
0.578
(1.00)
0.808
(1.00)
0.665
(1.00)
0.422
(1.00)
0.669
(1.00)
0.031
(1.00)
0.213
(1.00)
0.173
(1.00)
0.0248
(1.00)
0.144
(1.00)
Del Peak 9(3q26 31) 0 (0%) 519 0.704
(1.00)
0.996
(1.00)
0.874
(1.00)
0.12
(1.00)
0.0425
(1.00)
0.216
(1.00)
0.325
(1.00)
0.0202
(1.00)
0.191
(1.00)
0.492
(1.00)
0.00239
(1.00)
Del Peak 11(4q22 1) 0 (0%) 377 0.197
(1.00)
0.42
(1.00)
0.00417
(1.00)
0.188
(1.00)
0.00139
(1.00)
0.00114
(0.867)
0.362
(1.00)
0.00344
(1.00)
0.713
(1.00)
0.00265
(1.00)
0.0535
(1.00)
Del Peak 12(4q35 1) 0 (0%) 364 0.282
(1.00)
0.303
(1.00)
0.0325
(1.00)
0.862
(1.00)
0.0205
(1.00)
0.00185
(1.00)
0.638
(1.00)
0.0674
(1.00)
0.658
(1.00)
0.024
(1.00)
0.241
(1.00)
Del Peak 13(5q11 2) 0 (0%) 435 0.159
(1.00)
0.0866
(1.00)
0.0389
(1.00)
0.922
(1.00)
0.0271
(1.00)
0.00103
(0.789)
0.0224
(1.00)
0.0373
(1.00)
0.595
(1.00)
0.0234
(1.00)
0.0266
(1.00)
Del Peak 14(5q22 2) 0 (0%) 403 0.082
(1.00)
0.359
(1.00)
0.155
(1.00)
0.524
(1.00)
0.0622
(1.00)
0.000382
(0.301)
0.03
(1.00)
0.0584
(1.00)
0.21
(1.00)
0.147
(1.00)
0.0684
(1.00)
Del Peak 15(6p25 3) 0 (0%) 497 0.599
(1.00)
0.0683
(1.00)
1
(1.00)
0.0885
(1.00)
0.546
(1.00)
0.351
(1.00)
0.324
(1.00)
0.477
(1.00)
0.329
(1.00)
0.734
(1.00)
0.664
(1.00)
Del Peak 16(6q26) 0 (0%) 485 0.032
(1.00)
0.9
(1.00)
0.368
(1.00)
0.302
(1.00)
0.0479
(1.00)
0.637
(1.00)
0.038
(1.00)
0.041
(1.00)
0.0939
(1.00)
0.0091
(1.00)
0.109
(1.00)
Del Peak 17(7q31 1) 0 (0%) 560 0.918
(1.00)
0.329
(1.00)
1
(1.00)
0.305
(1.00)
0.503
(1.00)
1
(1.00)
0.332
(1.00)
0.696
(1.00)
0.723
(1.00)
0.606
(1.00)
0.849
(1.00)
Del Peak 20(8p11 21) 0 (0%) 451 0.599
(1.00)
0.329
(1.00)
0.031
(1.00)
0.478
(1.00)
0.163
(1.00)
0.414
(1.00)
0.0806
(1.00)
0.0364
(1.00)
0.117
(1.00)
0.0914
(1.00)
0.077
(1.00)
Del Peak 21(8q11 1) 0 (0%) 531 0.891
(1.00)
0.382
(1.00)
0.16
(1.00)
0.208
(1.00)
0.413
(1.00)
0.514
(1.00)
0.00198
(1.00)
0.047
(1.00)
0.376
(1.00)
0.292
(1.00)
0.0335
(1.00)
Del Peak 22(9p24 2) 0 (0%) 497 0.00182
(1.00)
0.12
(1.00)
0.496
(1.00)
0.0513
(1.00)
0.452
(1.00)
0.351
(1.00)
0.0227
(1.00)
0.0662
(1.00)
0.117
(1.00)
0.228
(1.00)
0.496
(1.00)
Del Peak 23(10p15 3) 0 (0%) 473 0.548
(1.00)
0.0282
(1.00)
0.271
(1.00)
0.913
(1.00)
0.361
(1.00)
0.00145
(1.00)
0.178
(1.00)
0.0241
(1.00)
0.949
(1.00)
0.0444
(1.00)
0.0672
(1.00)
Del Peak 24(10q21 1) 0 (0%) 457 0.852
(1.00)
0.0152
(1.00)
0.421
(1.00)
0.535
(1.00)
0.118
(1.00)
0.00326
(1.00)
0.681
(1.00)
0.0945
(1.00)
0.393
(1.00)
0.163
(1.00)
0.18
(1.00)
Del Peak 25(10q23 31) 0 (0%) 430 0.553
(1.00)
0.00668
(1.00)
0.0408
(1.00)
0.923
(1.00)
0.0205
(1.00)
0.0013
(0.986)
0.0614
(1.00)
0.0119
(1.00)
0.491
(1.00)
0.188
(1.00)
0.0508
(1.00)
Del Peak 26(10q25 2) 0 (0%) 435 0.779
(1.00)
0.0715
(1.00)
0.128
(1.00)
0.846
(1.00)
0.0322
(1.00)
0.00103
(0.789)
0.427
(1.00)
0.0114
(1.00)
0.459
(1.00)
0.161
(1.00)
0.165
(1.00)
Del Peak 27(11q22 3) 0 (0%) 471 0.502
(1.00)
0.396
(1.00)
0.086
(1.00)
0.587
(1.00)
0.0522
(1.00)
0.061
(1.00)
0.654
(1.00)
0.0114
(1.00)
0.631
(1.00)
0.0442
(1.00)
0.759
(1.00)
Del Peak 28(12p13 1) 0 (0%) 498 0.464
(1.00)
0.472
(1.00)
0.0256
(1.00)
0.326
(1.00)
0.000673
(0.521)
0.344
(1.00)
0.0985
(1.00)
0.229
(1.00)
0.768
(1.00)
0.921
(1.00)
0.589
(1.00)
Del Peak 29(12q21 2) 0 (0%) 495 0.669
(1.00)
0.709
(1.00)
0.0779
(1.00)
0.631
(1.00)
0.00833
(1.00)
0.117
(1.00)
0.0906
(1.00)
0.0551
(1.00)
1
(1.00)
0.0825
(1.00)
0.0947
(1.00)
Del Peak 31(15q11 2) 0 (0%) 342 0.77
(1.00)
0.618
(1.00)
0.216
(1.00)
0.551
(1.00)
0.0552
(1.00)
0.035
(1.00)
0.258
(1.00)
0.0889
(1.00)
0.888
(1.00)
0.0606
(1.00)
0.0877
(1.00)
Del Peak 32(15q21 1) 0 (0%) 348 0.435
(1.00)
0.603
(1.00)
0.0355
(1.00)
0.306
(1.00)
0.0252
(1.00)
0.0327
(1.00)
0.222
(1.00)
0.0842
(1.00)
0.559
(1.00)
0.0553
(1.00)
0.218
(1.00)
Del Peak 33(15q22 33) 0 (0%) 358 0.552
(1.00)
0.327
(1.00)
0.012
(1.00)
0.73
(1.00)
0.00583
(1.00)
0.00229
(1.00)
0.205
(1.00)
0.058
(1.00)
0.7
(1.00)
0.0284
(1.00)
0.013
(1.00)
Del Peak 35(16q23 1) 0 (0%) 503 0.00152
(1.00)
0.264
(1.00)
0.402
(1.00)
0.165
(1.00)
0.508
(1.00)
1
(1.00)
0.95
(1.00)
0.466
(1.00)
0.941
(1.00)
0.25
(1.00)
0.322
(1.00)
Del Peak 37(17q24 3) 0 (0%) 491 0.718
(1.00)
0.305
(1.00)
0.793
(1.00)
0.124
(1.00)
0.989
(1.00)
0.626
(1.00)
0.348
(1.00)
0.00108
(0.827)
0.316
(1.00)
0.043
(1.00)
0.123
(1.00)
Del Peak 42(19p13 3) 0 (0%) 483 0.396
(1.00)
0.183
(1.00)
0.0305
(1.00)
0.734
(1.00)
0.0669
(1.00)
0.641
(1.00)
0.0269
(1.00)
0.000979
(0.753)
0.179
(1.00)
0.00272
(1.00)
0.002
(1.00)
Del Peak 43(19q13 43) 0 (0%) 507 0.486
(1.00)
0.816
(1.00)
0.146
(1.00)
0.247
(1.00)
0.412
(1.00)
0.289
(1.00)
0.0703
(1.00)
0.101
(1.00)
0.812
(1.00)
0.0188
(1.00)
0.00724
(1.00)
Del Peak 44(20p12 1) 0 (0%) 396 0.106
(1.00)
0.631
(1.00)
0.0445
(1.00)
0.279
(1.00)
0.14
(1.00)
0.0632
(1.00)
0.83
(1.00)
0.623
(1.00)
0.438
(1.00)
0.793
(1.00)
0.257
(1.00)
Del Peak 45(20p12 1) 0 (0%) 396 0.106
(1.00)
0.631
(1.00)
0.0445
(1.00)
0.279
(1.00)
0.14
(1.00)
0.0632
(1.00)
0.83
(1.00)
0.623
(1.00)
0.438
(1.00)
0.793
(1.00)
0.257
(1.00)
Del Peak 46(21q11 2) 0 (0%) 380 0.534
(1.00)
0.721
(1.00)
0.00555
(1.00)
0.597
(1.00)
0.000621
(0.482)
0.175
(1.00)
0.606
(1.00)
0.307
(1.00)
0.73
(1.00)
0.00412
(1.00)
0.379
(1.00)
Del Peak 47(22q13 32) 0 (0%) 371 0.0441
(1.00)
0.672
(1.00)
0.173
(1.00)
0.861
(1.00)
0.0097
(1.00)
0.727
(1.00)
0.0266
(1.00)
0.00237
(1.00)
0.521
(1.00)
0.0109
(1.00)
0.036
(1.00)
'Amp Peak 2(2q33.1)' versus 'LYMPH.NODE.METASTASIS'

P value = 0.000238 (Chi-square test), Q value = 0.19

Table S1.  Gene #2: 'Amp Peak 2(2q33.1)' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 327 104 17 17 3 81 6 16 2
AMP PEAK 2(2Q33.1) CNV 55 18 9 4 0 25 2 8 1
AMP PEAK 2(2Q33.1) WILD-TYPE 272 86 8 13 3 56 4 8 1

Figure S1.  Get High-res Image Gene #2: 'Amp Peak 2(2q33.1)' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

'Amp Peak 6(7p21.3)' versus 'HISTOLOGICAL.TYPE'

P value = 0.000225 (Fisher's exact test), Q value = 0.18

Table S2.  Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
AMP PEAK 6(7P21.3) CNV 210 20 99 5
AMP PEAK 6(7P21.3) WILD-TYPE 147 34 44 8

Figure S2.  Get High-res Image Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 11(10q22.3)' versus 'LYMPH.NODE.METASTASIS'

P value = 2.77e-05 (Chi-square test), Q value = 0.022

Table S3.  Gene #11: 'Amp Peak 11(10q22.3)' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 327 104 17 17 3 81 6 16 2
AMP PEAK 11(10Q22.3) CNV 12 7 1 1 2 12 0 0 0
AMP PEAK 11(10Q22.3) WILD-TYPE 315 97 16 16 1 69 6 16 2

Figure S3.  Get High-res Image Gene #11: 'Amp Peak 11(10q22.3)' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

'Amp Peak 14(13q12.13)' versus 'HISTOLOGICAL.TYPE'

P value = 1.21e-09 (Fisher's exact test), Q value = 9.8e-07

Table S4.  Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
AMP PEAK 14(13Q12.13) CNV 233 16 112 5
AMP PEAK 14(13Q12.13) WILD-TYPE 124 38 31 8

Figure S4.  Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 15(13q12.2)' versus 'HISTOLOGICAL.TYPE'

P value = 2.65e-09 (Fisher's exact test), Q value = 2.2e-06

Table S5.  Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
AMP PEAK 15(13Q12.2) CNV 229 16 111 5
AMP PEAK 15(13Q12.2) WILD-TYPE 128 38 32 8

Figure S5.  Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 16(13q22.1)' versus 'HISTOLOGICAL.TYPE'

P value = 3.25e-08 (Fisher's exact test), Q value = 2.6e-05

Table S6.  Gene #16: 'Amp Peak 16(13q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
AMP PEAK 16(13Q22.1) CNV 235 18 109 4
AMP PEAK 16(13Q22.1) WILD-TYPE 122 36 34 9

Figure S6.  Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 24(20p11.21)' versus 'HISTOLOGICAL.TYPE'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.0092

Table S7.  Gene #24: 'Amp Peak 24(20p11.21)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
AMP PEAK 24(20P11.21) CNV 208 20 103 4
AMP PEAK 24(20P11.21) WILD-TYPE 149 34 40 9

Figure S7.  Get High-res Image Gene #24: 'Amp Peak 24(20p11.21)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 25(20q11.21)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.13e-06 (Fisher's exact test), Q value = 0.0074

Table S8.  Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 159
AMP PEAK 25(20Q11.21) CNV 295 141
AMP PEAK 25(20Q11.21) WILD-TYPE 117 18

Figure S8.  Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 25(20q11.21)' versus 'HISTOLOGICAL.TYPE'

P value = 7.95e-12 (Fisher's exact test), Q value = 6.5e-09

Table S9.  Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
AMP PEAK 25(20Q11.21) CNV 270 24 132 7
AMP PEAK 25(20Q11.21) WILD-TYPE 87 30 11 6

Figure S9.  Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 26(20q12)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.74e-06 (Fisher's exact test), Q value = 0.0038

Table S10.  Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 159
AMP PEAK 26(20Q12) CNV 296 142
AMP PEAK 26(20Q12) WILD-TYPE 116 17

Figure S10.  Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 26(20q12)' versus 'HISTOLOGICAL.TYPE'

P value = 5.41e-13 (Fisher's exact test), Q value = 4.4e-10

Table S11.  Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
AMP PEAK 26(20Q12) CNV 272 23 133 7
AMP PEAK 26(20Q12) WILD-TYPE 85 31 10 6

Figure S11.  Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 26(20q12)' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00019 (Chi-square test), Q value = 0.15

Table S12.  Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #12: '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 98 1 41 154 10 3 27 22 70 47 57 25 1
AMP PEAK 26(20Q12) CNV 74 1 24 107 5 3 19 21 55 40 51 24 0
AMP PEAK 26(20Q12) WILD-TYPE 24 0 17 47 5 0 8 1 15 7 6 1 1

Figure S12.  Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #12: 'NEOPLASM.DISEASESTAGE'

'Amp Peak 27(20q13.32)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.018

Table S13.  Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 159
AMP PEAK 27(20Q13.32) CNV 299 141
AMP PEAK 27(20Q13.32) WILD-TYPE 113 18

Figure S13.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 27(20q13.32)' versus 'HISTOLOGICAL.TYPE'

P value = 8.79e-12 (Fisher's exact test), Q value = 7.2e-09

Table S14.  Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
AMP PEAK 27(20Q13.32) CNV 274 24 132 7
AMP PEAK 27(20Q13.32) WILD-TYPE 83 30 11 6

Figure S14.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 10(4p16.1)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.022

Table S15.  Gene #38: 'Del Peak 10(4p16.1)' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients NO YES
ALL 9 566
DEL PEAK 10(4P16.1) CNV 9 173
DEL PEAK 10(4P16.1) WILD-TYPE 0 393

Figure S15.  Get High-res Image Gene #38: 'Del Peak 10(4p16.1)' versus Clinical Feature #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 18(8p23.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.4e-05 (Fisher's exact test), Q value = 0.019

Table S16.  Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 159
DEL PEAK 18(8P23.2) CNV 172 98
DEL PEAK 18(8P23.2) WILD-TYPE 240 61

Figure S16.  Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 18(8p23.2)' versus 'HISTOLOGICAL.TYPE'

P value = 2.72e-05 (Fisher's exact test), Q value = 0.022

Table S17.  Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
DEL PEAK 18(8P23.2) CNV 156 15 89 7
DEL PEAK 18(8P23.2) WILD-TYPE 201 39 54 6

Figure S17.  Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 18(8p23.2)' versus 'LYMPH.NODE.METASTASIS'

P value = 0.000164 (Chi-square test), Q value = 0.13

Table S18.  Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 327 104 17 17 3 81 6 16 2
DEL PEAK 18(8P23.2) CNV 129 57 10 7 1 55 1 9 2
DEL PEAK 18(8P23.2) WILD-TYPE 198 47 7 10 2 26 5 7 0

Figure S18.  Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

'Del Peak 19(8p22)' versus 'HISTOLOGICAL.TYPE'

P value = 0.000245 (Fisher's exact test), Q value = 0.19

Table S19.  Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
DEL PEAK 19(8P22) CNV 168 16 89 7
DEL PEAK 19(8P22) WILD-TYPE 189 38 54 6

Figure S19.  Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

P value = 1.79e-05 (Chi-square test), Q value = 0.014

Table S20.  Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 327 104 17 17 3 81 6 16 2
DEL PEAK 19(8P22) CNV 133 60 11 7 1 59 2 9 2
DEL PEAK 19(8P22) WILD-TYPE 194 44 6 10 2 22 4 7 0

Figure S20.  Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

'Del Peak 19(8p22)' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000114 (t-test), Q value = 0.091

Table S21.  Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 541 2.2 (4.7)
DEL PEAK 19(8P22) CNV 273 3.0 (5.7)
DEL PEAK 19(8P22) WILD-TYPE 268 1.4 (3.3)

Figure S21.  Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 30(14q22.1)' versus 'HISTOLOGICAL.TYPE'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00093

Table S22.  Gene #58: 'Del Peak 30(14q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
DEL PEAK 30(14Q22.1) CNV 115 4 62 1
DEL PEAK 30(14Q22.1) WILD-TYPE 242 50 81 12

Figure S22.  Get High-res Image Gene #58: 'Del Peak 30(14q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 34(16p13.3)' versus 'Time to Death'

P value = 8.33e-05 (logrank test), Q value = 0.067

Table S23.  Gene #62: 'Del Peak 34(16p13.3)' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 451 60 0.1 - 135.5 (7.0)
DEL PEAK 34(16P13.3) CNV 43 13 0.2 - 49.9 (8.2)
DEL PEAK 34(16P13.3) WILD-TYPE 408 47 0.1 - 135.5 (7.0)

Figure S23.  Get High-res Image Gene #62: 'Del Peak 34(16p13.3)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 36(17p12)' versus 'HISTOLOGICAL.TYPE'

P value = 6.55e-08 (Fisher's exact test), Q value = 5.3e-05

Table S24.  Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
DEL PEAK 36(17P12) CNV 213 14 103 6
DEL PEAK 36(17P12) WILD-TYPE 144 40 40 7

Figure S24.  Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 38(18p11.31)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.82e-06 (Fisher's exact test), Q value = 0.0015

Table S25.  Gene #66: 'Del Peak 38(18p11.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 159
DEL PEAK 38(18P11.31) CNV 219 119
DEL PEAK 38(18P11.31) WILD-TYPE 193 40

Figure S25.  Get High-res Image Gene #66: 'Del Peak 38(18p11.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 38(18p11.31)' versus 'HISTOLOGICAL.TYPE'

P value = 1.52e-16 (Fisher's exact test), Q value = 1.2e-13

Table S26.  Gene #66: 'Del Peak 38(18p11.31)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
DEL PEAK 38(18P11.31) CNV 211 7 113 6
DEL PEAK 38(18P11.31) WILD-TYPE 146 47 30 7

Figure S26.  Get High-res Image Gene #66: 'Del Peak 38(18p11.31)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 39(18q12.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.57e-09 (Fisher's exact test), Q value = 1.3e-06

Table S27.  Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 159
DEL PEAK 39(18Q12.2) CNV 247 136
DEL PEAK 39(18Q12.2) WILD-TYPE 165 23

Figure S27.  Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 39(18q12.2)' versus 'HISTOLOGICAL.TYPE'

P value = 8.26e-18 (Fisher's exact test), Q value = 6.8e-15

Table S28.  Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
DEL PEAK 39(18Q12.2) CNV 235 11 125 10
DEL PEAK 39(18Q12.2) WILD-TYPE 122 43 18 3

Figure S28.  Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 40(18q21.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.07e-09 (Fisher's exact test), Q value = 8.7e-07

Table S29.  Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 159
DEL PEAK 40(18Q21.2) CNV 260 140
DEL PEAK 40(18Q21.2) WILD-TYPE 152 19

Figure S29.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 40(18q21.2)' versus 'HISTOLOGICAL.TYPE'

P value = 3.54e-16 (Fisher's exact test), Q value = 2.9e-13

Table S30.  Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
DEL PEAK 40(18Q21.2) CNV 245 14 126 12
DEL PEAK 40(18Q21.2) WILD-TYPE 112 40 17 1

Figure S30.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 40(18q21.2)' versus 'LYMPH.NODE.METASTASIS'

P value = 0.000227 (Chi-square test), Q value = 0.18

Table S31.  Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

nPatients N0 N1 N1A N1B N1C N2 N2A N2B NX
ALL 327 104 17 17 3 81 6 16 2
DEL PEAK 40(18Q21.2) CNV 201 85 11 13 3 68 5 13 2
DEL PEAK 40(18Q21.2) WILD-TYPE 126 19 6 4 0 13 1 3 0

Figure S31.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #8: 'LYMPH.NODE.METASTASIS'

'Del Peak 40(18q21.2)' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.49e-05 (Chi-square test), Q value = 0.036

Table S32.  Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #12: '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 98 1 41 154 10 3 27 22 70 47 57 25 1
DEL PEAK 40(18Q21.2) CNV 58 0 25 96 4 3 17 18 54 39 51 22 1
DEL PEAK 40(18Q21.2) WILD-TYPE 40 1 16 58 6 0 10 4 16 8 6 3 0

Figure S32.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #12: 'NEOPLASM.DISEASESTAGE'

'Del Peak 41(18q22.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.94e-07 (Fisher's exact test), Q value = 0.00016

Table S33.  Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 412 159
DEL PEAK 41(18Q22.1) CNV 260 135
DEL PEAK 41(18Q22.1) WILD-TYPE 152 24

Figure S33.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 41(18q22.1)' versus 'HISTOLOGICAL.TYPE'

P value = 2.05e-15 (Fisher's exact test), Q value = 1.7e-12

Table S34.  Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 357 54 143 13
DEL PEAK 41(18Q22.1) CNV 246 13 124 10
DEL PEAK 41(18Q22.1) WILD-TYPE 111 41 19 3

Figure S34.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 41(18q22.1)' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000104 (Chi-square test), Q value = 0.083

Table S35.  Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #12: '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 98 1 41 154 10 3 27 22 70 47 57 25 1
DEL PEAK 41(18Q22.1) CNV 58 0 25 96 4 3 15 17 53 39 50 22 1
DEL PEAK 41(18Q22.1) WILD-TYPE 40 1 16 58 6 0 12 5 17 8 7 3 0

Figure S35.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #12: 'NEOPLASM.DISEASESTAGE'

Methods & Data
Input
  • Mutation data file = all_lesions.conf_99.cnv.cluster.txt

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

  • Number of patients = 575

  • Number of significantly arm-level cnvs = 75

  • Number of selected clinical features = 12

  • 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)