Correlation between copy number variation genes (focal) and selected clinical features
Colon/Rectal Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1ZK5DMJ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Colon/Rectal Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1ZK5DMJ
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, 53 significant findings detected with Q value < 0.25.

  • Amp Peak 5(6p21.1) cnv correlated to 'PATHOLOGY.N'.

  • Amp Peak 6(7p21.3) cnv correlated to 'HISTOLOGICAL.TYPE',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • Amp Peak 14(13q12.13) cnv correlated to 'HISTOLOGICAL.TYPE',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • Amp Peak 15(13q12.2) cnv correlated to 'HISTOLOGICAL.TYPE',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

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

  • Amp Peak 18(16p11.2) cnv correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.

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

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

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

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

  • 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',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • Del Peak 19(8p22) cnv correlated to 'HISTOLOGICAL.TYPE',  'PATHOLOGY.N',  'TUMOR.STAGE', 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',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • 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',  'HISTOLOGICAL.TYPE',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • Del Peak 40(18q21.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'HISTOLOGICAL.TYPE',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • Del Peak 41(18q22.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'HISTOLOGICAL.TYPE',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • Del Peak 42(19p13.3) 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 75 arm-level results and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 53 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test t-test
Del Peak 18(8p23 2) 0 (0%) 303 0.619
(1.00) 		0.205
(1.00) 		2.4e-05
(0.0209) 		0.18
(1.00) 		2.9e-05
(0.0252) 		0.081
(1.00) 		2.78e-05
(0.0242) 		0.00989
(1.00) 		3.4e-05
(0.0294) 		0.0155
(1.00) 		0.00536
(1.00) 		0.000422
(0.356)
Del Peak 19(8p22) 0 (0%) 290 0.597
(1.00) 		0.317
(1.00) 		0.000379
(0.321) 		0.403
(1.00) 		0.000256
(0.217) 		0.0753
(1.00) 		1.97e-06
(0.00173) 		0.00381
(1.00) 		1.24e-06
(0.0011) 		0.0196
(1.00) 		0.00797
(1.00) 		0.000106
(0.0907)
Del Peak 39(18q12 2) 0 (0%) 189 0.942
(1.00) 		0.0817
(1.00) 		1.57e-09
(1.4e-06) 		0.477
(1.00) 		8.59e-18
(7.73e-15) 		0.421
(1.00) 		0.000131
(0.112) 		0.00447
(1.00) 		6.82e-05
(0.0587) 		0.034
(1.00) 		0.0373
(1.00) 		0.00847
(1.00)
Del Peak 40(18q21 2) 0 (0%) 172 0.481
(1.00) 		0.0823
(1.00) 		1.07e-09
(9.55e-07) 		0.145
(1.00) 		3.7e-16
(3.32e-13) 		0.315
(1.00) 		1.95e-06
(0.00172) 		0.00162
(1.00) 		4.1e-07
(0.000363) 		0.0637
(1.00) 		0.0438
(1.00) 		0.000978
(0.811)
Del Peak 41(18q22 1) 0 (0%) 177 0.332
(1.00) 		0.221
(1.00) 		1.94e-07
(0.000172) 		0.239
(1.00) 		2.07e-15
(1.86e-12) 		0.444
(1.00) 		1.14e-05
(0.01) 		0.00238
(1.00) 		4.68e-06
(0.00411) 		0.0632
(1.00) 		0.0824
(1.00) 		0.00182
(1.00)
Amp Peak 6(7p21 3) 0 (0%) 238 0.304
(1.00) 		0.103
(1.00) 		0.0292
(1.00) 		0.734
(1.00) 		0.000225
(0.191) 		0.889
(1.00) 		1.23e-05
(0.0107) 		0.0274
(1.00) 		4.42e-06
(0.00389) 		0.0882
(1.00) 		0.0892
(1.00) 		0.0339
(1.00)
Amp Peak 14(13q12 13) 0 (0%) 204 0.126
(1.00) 		0.314
(1.00) 		0.00246
(1.00) 		0.727
(1.00) 		1.18e-09
(1.05e-06) 		0.561
(1.00) 		3.88e-05
(0.0336) 		0.0101
(1.00) 		7.49e-05
(0.0644) 		1
(1.00) 		0.0288
(1.00) 		0.0342
(1.00)
Amp Peak 15(13q12 2) 0 (0%) 209 0.101
(1.00) 		0.239
(1.00) 		0.00188
(1.00) 		0.543
(1.00) 		2.61e-09
(2.32e-06) 		0.533
(1.00) 		9.03e-05
(0.0774) 		0.023
(1.00) 		0.000184
(0.156) 		1
(1.00) 		0.051
(1.00) 		0.0355
(1.00)
Amp Peak 25(20q11 21) 0 (0%) 136 0.317
(1.00) 		0.823
(1.00) 		9.13e-06
(0.008) 		0.376
(1.00) 		7.88e-12
(7.05e-09) 		0.506
(1.00) 		0.00141
(1.00) 		0.00533
(1.00) 		0.000107
(0.0916) 		0.693
(1.00) 		0.0588
(1.00) 		0.344
(1.00)
Amp Peak 26(20q12) 0 (0%) 134 0.274
(1.00) 		0.726
(1.00) 		4.74e-06
(0.00416) 		0.374
(1.00) 		5.38e-13
(4.82e-10) 		0.611
(1.00) 		0.00101
(0.84) 		0.00129
(1.00) 		4.17e-05
(0.036) 		0.692
(1.00) 		0.059
(1.00) 		0.393
(1.00)
Amp Peak 27(20q13 32) 0 (0%) 131 0.369
(1.00) 		0.658
(1.00) 		2.18e-05
(0.019) 		0.551
(1.00) 		8.76e-12
(7.83e-09) 		0.588
(1.00) 		0.00158
(1.00) 		0.00424
(1.00) 		0.000131
(0.112) 		0.692
(1.00) 		0.0589
(1.00) 		0.246
(1.00)
Del Peak 36(17p12) 0 (0%) 232 0.656
(1.00) 		0.0983
(1.00) 		0.00169
(1.00) 		0.609
(1.00) 		6.48e-08
(5.75e-05) 		0.419
(1.00) 		0.000121
(0.104) 		0.041
(1.00) 		3.15e-05
(0.0273) 		0.325
(1.00) 		0.119
(1.00) 		0.00223
(1.00)
Amp Peak 16(13q22 1) 0 (0%) 204 0.0454
(1.00) 		0.444
(1.00) 		0.0249
(1.00) 		0.221
(1.00) 		3.13e-08
(2.78e-05) 		0.736
(1.00) 		0.000127
(0.108) 		0.024
(1.00) 		0.0006
(0.504) 		0.503
(1.00) 		0.162
(1.00) 		0.185
(1.00)
Amp Peak 18(16p11 2) 0 (0%) 414 0.838
(1.00) 		0.26
(1.00) 		0.918
(1.00) 		0.71
(1.00) 		0.0024
(1.00) 		0.721
(1.00) 		5.82e-05
(0.0502) 		0.111
(1.00) 		8.54e-05
(0.0733) 		0.715
(1.00) 		0.394
(1.00) 		0.0175
(1.00)
Del Peak 38(18p11 31) 0 (0%) 234 0.98
(1.00) 		0.059
(1.00) 		1.82e-06
(0.00161) 		1
(1.00) 		1.53e-16
(1.37e-13) 		0.882
(1.00) 		0.0106
(1.00) 		0.000584
(0.492) 		0.000895
(0.743) 		0.322
(1.00) 		0.024
(1.00) 		0.457
(1.00)
Amp Peak 5(6p21 1) 0 (0%) 429 0.489
(1.00) 		0.682
(1.00) 		0.0314
(1.00) 		0.15
(1.00) 		0.00236
(1.00) 		0.215
(1.00) 		3.17e-05
(0.0275) 		0.109
(1.00) 		0.000331
(0.28) 		0.00136
(1.00) 		0.145
(1.00) 		0.00273
(1.00)
Amp Peak 24(20p11 21) 0 (0%) 236 0.808
(1.00) 		0.709
(1.00) 		0.00784
(1.00) 		0.0413
(1.00) 		1.12e-05
(0.00984) 		0.885
(1.00) 		0.382
(1.00) 		0.00312
(1.00) 		0.0516
(1.00) 		0.32
(1.00) 		0.696
(1.00) 		0.93
(1.00)
Del Peak 10(4p16 1) 0 (0%) 393 0.0406
(1.00) 		0.954
(1.00) 		0.0561
(1.00) 		0.128
(1.00) 		0.0277
(1.00) 		0.985
(1.00) 		0.00057
(0.48) 		0.0131
(1.00) 		0.00164
(1.00) 		2.78e-05
(0.0242) 		0.0821
(1.00) 		0.0016
(1.00)
Del Peak 30(14q22 1) 0 (0%) 390 0.208
(1.00) 		0.233
(1.00) 		0.0212
(1.00) 		0.421
(1.00) 		1.15e-06
(0.00101) 		0.78
(1.00) 		0.00362
(1.00) 		0.145
(1.00) 		0.175
(1.00) 		0.725
(1.00) 		0.539
(1.00) 		0.691
(1.00)
Del Peak 34(16p13 3) 0 (0%) 517 4.34e-05
(0.0375) 		0.254
(1.00) 		0.359
(1.00) 		0.89
(1.00) 		0.418
(1.00) 		0.0689
(1.00) 		0.132
(1.00) 		0.381
(1.00) 		0.101
(1.00) 		0.609
(1.00) 		0.749
(1.00) 		0.0606
(1.00)
Del Peak 42(19p13 3) 0 (0%) 483 0.406
(1.00) 		0.183
(1.00) 		0.0305
(1.00) 		0.733
(1.00) 		0.0678
(1.00) 		0.407
(1.00) 		7.64e-05
(0.0656) 		0.0275
(1.00) 		0.00312
(1.00) 		0.641
(1.00) 		0.13
(1.00) 		0.0025
(1.00)
Amp Peak 1(1q31 1) 0 (0%) 441 0.466
(1.00) 		0.292
(1.00) 		0.0268
(1.00) 		0.236
(1.00) 		0.0946
(1.00) 		0.381
(1.00) 		0.0539
(1.00) 		0.175
(1.00) 		0.0343
(1.00) 		0.0357
(1.00) 		0.503
(1.00) 		0.0152
(1.00)
Amp Peak 2(2q33 1) 0 (0%) 452 0.135
(1.00) 		0.385
(1.00) 		0.031
(1.00) 		1
(1.00) 		0.00379
(1.00) 		0.686
(1.00) 		0.00128
(1.00) 		0.541
(1.00) 		0.0227
(1.00) 		0.103
(1.00) 		0.516
(1.00) 		0.0246
(1.00)
Amp Peak 3(5p12) 0 (0%) 468 0.0162
(1.00) 		0.372
(1.00) 		0.151
(1.00) 		0.748
(1.00) 		0.0568
(1.00) 		0.396
(1.00) 		0.0431
(1.00) 		0.354
(1.00) 		0.191
(1.00) 		0.379
(1.00) 		0.0289
(1.00) 		0.0708
(1.00)
Amp Peak 4(5q22 3) 0 (0%) 516 0.75
(1.00) 		0.865
(1.00) 		0.445
(1.00) 		0.891
(1.00) 		0.316
(1.00) 		0.907
(1.00) 		0.176
(1.00) 		0.032
(1.00) 		0.12
(1.00) 		1
(1.00) 		0.0798
(1.00) 		0.492
(1.00)
Amp Peak 7(8p11 23) 0 (0%) 379 0.472
(1.00) 		0.752
(1.00) 		0.625
(1.00) 		0.482
(1.00) 		0.232
(1.00) 		0.409
(1.00) 		0.503
(1.00) 		0.413
(1.00) 		0.88
(1.00) 		0.498
(1.00) 		0.175
(1.00) 		0.633
(1.00)
Amp Peak 8(8p11 21) 0 (0%) 337 0.633
(1.00) 		0.597
(1.00) 		0.636
(1.00) 		0.204
(1.00) 		0.12
(1.00) 		0.5
(1.00) 		0.333
(1.00) 		0.305
(1.00) 		0.475
(1.00) 		0.742
(1.00) 		0.0277
(1.00) 		0.409
(1.00)
Amp Peak 9(8q12 1) 0 (0%) 266 0.907
(1.00) 		0.19
(1.00) 		0.303
(1.00) 		0.615
(1.00) 		0.0093
(1.00) 		0.128
(1.00) 		0.0853
(1.00) 		0.0256
(1.00) 		0.0726
(1.00) 		0.0423
(1.00) 		0.0328
(1.00) 		0.027
(1.00)
Amp Peak 10(8q24 21) 0 (0%) 230 0.545
(1.00) 		0.236
(1.00) 		0.0863
(1.00) 		0.394
(1.00) 		0.0113
(1.00) 		0.143
(1.00) 		0.171
(1.00) 		0.0551
(1.00) 		0.233
(1.00) 		0.0931
(1.00) 		0.0997
(1.00) 		0.0585
(1.00)
Amp Peak 11(10q22 3) 0 (0%) 540 0.819
(1.00) 		0.303
(1.00) 		1
(1.00) 		0.487
(1.00) 		0.932
(1.00) 		0.141
(1.00) 		0.00814
(1.00) 		0.912
(1.00) 		0.116
(1.00) 		0.434
(1.00) 		0.91
(1.00) 		0.0883
(1.00)
Amp Peak 12(11p15 5) 0 (0%) 446 0.709
(1.00) 		0.0608
(1.00) 		0.145
(1.00) 		0.549
(1.00) 		0.00144
(1.00) 		0.293
(1.00) 		0.712
(1.00) 		0.385
(1.00) 		0.808
(1.00) 		0.12
(1.00) 		0.706
(1.00) 		0.42
(1.00)
Amp Peak 13(12p13 32) 0 (0%) 431 0.26
(1.00) 		0.0696
(1.00) 		0.829
(1.00) 		0.5
(1.00) 		0.351
(1.00) 		0.387
(1.00) 		0.0536
(1.00) 		0.0859
(1.00) 		0.0625
(1.00) 		0.698
(1.00) 		0.612
(1.00) 		0.442
(1.00)
Amp Peak 17(15q26 1) 0 (0%) 532 0.0824
(1.00) 		0.753
(1.00) 		0.291
(1.00) 		0.0582
(1.00) 		0.433
(1.00) 		0.287
(1.00) 		0.00409
(1.00) 		0.649
(1.00) 		0.198
(1.00) 		0.141
(1.00) 		0.38
(1.00) 		0.0562
(1.00)
Amp Peak 19(17q12) 0 (0%) 431 0.489
(1.00) 		0.363
(1.00) 		0.591
(1.00) 		0.101
(1.00) 		0.457
(1.00) 		0.417
(1.00) 		0.152
(1.00) 		0.0117
(1.00) 		0.0158
(1.00) 		0.462
(1.00) 		0.0311
(1.00) 		0.345
(1.00)
Amp Peak 20(17q24 1) 0 (0%) 447 0.0431
(1.00) 		0.245
(1.00) 		0.911
(1.00) 		0.617
(1.00) 		0.0878
(1.00) 		0.771
(1.00) 		0.886
(1.00) 		0.0549
(1.00) 		0.219
(1.00) 		0.691
(1.00) 		0.0941
(1.00) 		0.689
(1.00)
Amp Peak 21(19p13 2) 0 (0%) 478 0.144
(1.00) 		0.493
(1.00) 		0.216
(1.00) 		0.182
(1.00) 		0.0516
(1.00) 		0.409
(1.00) 		0.0339
(1.00) 		0.233
(1.00) 		0.126
(1.00) 		1
(1.00) 		0.184
(1.00) 		0.972
(1.00)
Amp Peak 22(19q12) 0 (0%) 453 0.628
(1.00) 		0.941
(1.00) 		0.256
(1.00) 		0.185
(1.00) 		0.0293
(1.00) 		0.654
(1.00) 		0.0943
(1.00) 		0.139
(1.00) 		0.226
(1.00) 		0.692
(1.00) 		0.592
(1.00) 		0.419
(1.00)
Amp Peak 23(20p11 23) 0 (0%) 274 0.699
(1.00) 		0.921
(1.00) 		0.0194
(1.00) 		0.0364
(1.00) 		0.00072
(0.601) 		0.873
(1.00) 		0.0368
(1.00) 		0.00134
(1.00) 		0.011
(1.00) 		0.181
(1.00) 		0.383
(1.00) 		0.305
(1.00)
Amp Peak 28(Xq28) 0 (0%) 454 0.245
(1.00) 		0.209
(1.00) 		0.421
(1.00) 		0.838
(1.00) 		0.0249
(1.00) 		0.521
(1.00) 		0.017
(1.00) 		0.219
(1.00) 		0.0635
(1.00) 		0.693
(1.00) 		0.29
(1.00) 		0.286
(1.00)
Del Peak 1(1p36 11) 0 (0%) 353 0.051
(1.00) 		0.105
(1.00) 		0.126
(1.00) 		0.392
(1.00) 		0.00644
(1.00) 		0.238
(1.00) 		0.000887
(0.737) 		0.000615
(0.516) 		0.000734
(0.611) 		0.739
(1.00) 		0.0585
(1.00) 		0.000594
(0.5)
Del Peak 2(1p33) 0 (0%) 419 0.0178
(1.00) 		0.836
(1.00) 		0.401
(1.00) 		0.851
(1.00) 		0.0797
(1.00) 		0.226
(1.00) 		0.00507
(1.00) 		0.0106
(1.00) 		0.0159
(1.00) 		0.709
(1.00) 		0.138
(1.00) 		0.0154
(1.00)
Del Peak 3(1p13 2) 0 (0%) 418 0.0696
(1.00) 		0.841
(1.00) 		0.248
(1.00) 		0.639
(1.00) 		0.135
(1.00) 		0.15
(1.00) 		0.00213
(1.00) 		0.00127
(1.00) 		0.0162
(1.00) 		0.265
(1.00) 		0.205
(1.00) 		0.00297
(1.00)
Del Peak 4(2p12) 0 (0%) 555 0.796
(1.00) 		0.179
(1.00) 		0.00346
(1.00) 		0.821
(1.00) 		0.0208
(1.00) 		1
(1.00) 		0.351
(1.00) 		0.56
(1.00) 		0.329
(1.00) 		0.275
(1.00) 		0.876
(1.00) 		0.318
(1.00)
Del Peak 5(2q22 1) 0 (0%) 542 0.85
(1.00) 		0.564
(1.00) 		0.842
(1.00) 		0.474
(1.00) 		0.927
(1.00) 		0.669
(1.00) 		0.609
(1.00) 		0.689
(1.00) 		0.174
(1.00) 		1
(1.00) 		1
(1.00) 		0.894
(1.00)
Del Peak 6(2q37 2) 0 (0%) 545 0.842
(1.00) 		0.139
(1.00) 		0.835
(1.00) 		0.458
(1.00) 		0.945
(1.00) 		0.344
(1.00) 		0.208
(1.00) 		0.133
(1.00) 		0.0449
(1.00) 		1
(1.00) 		1
(1.00) 		0.859
(1.00)
Del Peak 7(3p26 3) 0 (0%) 491 0.000643
(0.538) 		0.855
(1.00) 		0.691
(1.00) 		0.723
(1.00) 		0.19
(1.00) 		0.0373
(1.00) 		0.0192
(1.00) 		0.00105
(0.865) 		0.000684
(0.571) 		0.131
(1.00) 		0.0674
(1.00) 		0.0296
(1.00)
Del Peak 8(3p14 2) 0 (0%) 471 0.216
(1.00) 		0.578
(1.00) 		0.808
(1.00) 		0.664
(1.00) 		0.416
(1.00) 		0.136
(1.00) 		0.181
(1.00) 		0.0317
(1.00) 		0.0461
(1.00) 		0.669
(1.00) 		0.123
(1.00) 		0.0236
(1.00)
Del Peak 9(3q26 31) 0 (0%) 519 0.714
(1.00) 		0.996
(1.00) 		0.874
(1.00) 		0.0931
(1.00) 		0.0423
(1.00) 		0.0139
(1.00) 		0.371
(1.00) 		0.327
(1.00) 		0.00215
(1.00) 		0.216
(1.00) 		0.111
(1.00) 		0.504
(1.00)
Del Peak 11(4q22 1) 0 (0%) 377 0.193
(1.00) 		0.42
(1.00) 		0.00417
(1.00) 		0.187
(1.00) 		0.00142
(1.00) 		0.134
(1.00) 		0.0018
(1.00) 		0.369
(1.00) 		0.0375
(1.00) 		0.00114
(0.937) 		0.426
(1.00) 		0.00264
(1.00)
Del Peak 12(4q35 1) 0 (0%) 364 0.277
(1.00) 		0.303
(1.00) 		0.0325
(1.00) 		0.863
(1.00) 		0.021
(1.00) 		0.702
(1.00) 		0.00325
(1.00) 		0.645
(1.00) 		0.118
(1.00) 		0.00185
(1.00) 		0.788
(1.00) 		0.0218
(1.00)
Del Peak 13(5q11 2) 0 (0%) 435 0.164
(1.00) 		0.0866
(1.00) 		0.0389
(1.00) 		1
(1.00) 		0.0275
(1.00) 		0.976
(1.00) 		0.0078
(1.00) 		0.0232
(1.00) 		0.0344
(1.00) 		0.00103
(0.851) 		0.271
(1.00) 		0.0226
(1.00)
Del Peak 14(5q22 2) 0 (0%) 403 0.0866
(1.00) 		0.359
(1.00) 		0.155
(1.00) 		0.648
(1.00) 		0.0624
(1.00) 		0.773
(1.00) 		0.0168
(1.00) 		0.0311
(1.00) 		0.0332
(1.00) 		0.000382
(0.322) 		0.103
(1.00) 		0.145
(1.00)
Del Peak 15(6p25 3) 0 (0%) 497 0.611
(1.00) 		0.0683
(1.00) 		1
(1.00) 		0.0876
(1.00) 		0.544
(1.00) 		0.261
(1.00) 		0.534
(1.00) 		0.326
(1.00) 		0.223
(1.00) 		0.351
(1.00) 		0.324
(1.00) 		0.749
(1.00)
Del Peak 16(6q26) 0 (0%) 485 0.029
(1.00) 		0.9
(1.00) 		0.368
(1.00) 		0.301
(1.00) 		0.0485
(1.00) 		0.0584
(1.00) 		0.0136
(1.00) 		0.0389
(1.00) 		0.594
(1.00) 		0.637
(1.00) 		0.0625
(1.00) 		0.00961
(1.00)
Del Peak 17(7q31 1) 0 (0%) 560 1
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.307
(1.00) 		0.503
(1.00) 		0.525
(1.00) 		0.673
(1.00) 		0.33
(1.00) 		0.342
(1.00) 		1
(1.00) 		0.706
(1.00) 		0.61
(1.00)
Del Peak 20(8p11 21) 0 (0%) 451 0.598
(1.00) 		0.329
(1.00) 		0.031
(1.00) 		0.542
(1.00) 		0.167
(1.00) 		0.535
(1.00) 		0.00723
(1.00) 		0.0823
(1.00) 		0.027
(1.00) 		0.414
(1.00) 		0.0885
(1.00) 		0.0888
(1.00)
Del Peak 21(8q11 1) 0 (0%) 531 0.889
(1.00) 		0.382
(1.00) 		0.16
(1.00) 		0.208
(1.00) 		0.418
(1.00) 		0.714
(1.00) 		0.0274
(1.00) 		0.00202
(1.00) 		0.0962
(1.00) 		0.514
(1.00) 		0.418
(1.00) 		0.302
(1.00)
Del Peak 22(9p24 2) 0 (0%) 497 0.00207
(1.00) 		0.12
(1.00) 		0.496
(1.00) 		0.0507
(1.00) 		0.452
(1.00) 		0.497
(1.00) 		0.136
(1.00) 		0.0231
(1.00) 		0.291
(1.00) 		0.351
(1.00) 		0.0396
(1.00) 		0.237
(1.00)
Del Peak 23(10p15 3) 0 (0%) 473 0.577
(1.00) 		0.0282
(1.00) 		0.271
(1.00) 		0.913
(1.00) 		0.364
(1.00) 		0.721
(1.00) 		0.00713
(1.00) 		0.181
(1.00) 		0.00847
(1.00) 		0.00145
(1.00) 		1
(1.00) 		0.0465
(1.00)
Del Peak 24(10q21 1) 0 (0%) 457 0.869
(1.00) 		0.0152
(1.00) 		0.421
(1.00) 		0.535
(1.00) 		0.118
(1.00) 		0.723
(1.00) 		0.164
(1.00) 		0.682
(1.00) 		0.368
(1.00) 		0.00326
(1.00) 		0.167
(1.00) 		0.17
(1.00)
Del Peak 25(10q23 31) 0 (0%) 430 0.566
(1.00) 		0.00668
(1.00) 		0.0408
(1.00) 		0.923
(1.00) 		0.0208
(1.00) 		0.206
(1.00) 		0.0139
(1.00) 		0.0621
(1.00) 		0.0977
(1.00) 		0.0013
(1.00) 		0.431
(1.00) 		0.201
(1.00)
Del Peak 26(10q25 2) 0 (0%) 435 0.756
(1.00) 		0.0715
(1.00) 		0.128
(1.00) 		0.846
(1.00) 		0.0324
(1.00) 		0.218
(1.00) 		0.0134
(1.00) 		0.43
(1.00) 		0.116
(1.00) 		0.00103
(0.851) 		0.396
(1.00) 		0.172
(1.00)
Del Peak 27(11q22 3) 0 (0%) 471 0.473
(1.00) 		0.396
(1.00) 		0.086
(1.00) 		0.588
(1.00) 		0.0532
(1.00) 		0.39
(1.00) 		0.0514
(1.00) 		0.633
(1.00) 		0.0927
(1.00) 		0.061
(1.00) 		0.63
(1.00) 		0.0422
(1.00)
Del Peak 28(12p13 1) 0 (0%) 498 0.466
(1.00) 		0.472
(1.00) 		0.0256
(1.00) 		0.327
(1.00) 		0.000677
(0.566) 		0.501
(1.00) 		0.0319
(1.00) 		0.1
(1.00) 		0.208
(1.00) 		0.344
(1.00) 		0.557
(1.00) 		0.957
(1.00)
Del Peak 29(12q21 2) 0 (0%) 495 0.636
(1.00) 		0.709
(1.00) 		0.0779
(1.00) 		0.717
(1.00) 		0.00837
(1.00) 		0.675
(1.00) 		0.0185
(1.00) 		0.0916
(1.00) 		0.239
(1.00) 		0.117
(1.00) 		1
(1.00) 		0.0773
(1.00)
Del Peak 31(15q11 2) 0 (0%) 342 0.771
(1.00) 		0.618
(1.00) 		0.216
(1.00) 		0.496
(1.00) 		0.0549
(1.00) 		0.804
(1.00) 		0.0148
(1.00) 		0.264
(1.00) 		0.0414
(1.00) 		0.035
(1.00) 		0.68
(1.00) 		0.0616
(1.00)
Del Peak 32(15q21 1) 0 (0%) 348 0.434
(1.00) 		0.603
(1.00) 		0.0355
(1.00) 		0.305
(1.00) 		0.0247
(1.00) 		0.846
(1.00) 		0.0271
(1.00) 		0.228
(1.00) 		0.125
(1.00) 		0.0327
(1.00) 		0.704
(1.00) 		0.0512
(1.00)
Del Peak 33(15q22 33) 0 (0%) 358 0.555
(1.00) 		0.327
(1.00) 		0.012
(1.00) 		0.667
(1.00) 		0.00595
(1.00) 		0.0968
(1.00) 		0.00679
(1.00) 		0.211
(1.00) 		0.0235
(1.00) 		0.00229
(1.00) 		0.832
(1.00) 		0.0287
(1.00)
Del Peak 35(16q23 1) 0 (0%) 503 0.0014
(1.00) 		0.264
(1.00) 		0.402
(1.00) 		0.167
(1.00) 		0.515
(1.00) 		0.252
(1.00) 		0.775
(1.00) 		0.951
(1.00) 		0.465
(1.00) 		1
(1.00) 		0.926
(1.00) 		0.239
(1.00)
Del Peak 37(17q24 3) 0 (0%) 491 0.731
(1.00) 		0.305
(1.00) 		0.793
(1.00) 		0.0994
(1.00) 		0.99
(1.00) 		0.243
(1.00) 		0.0075
(1.00) 		0.352
(1.00) 		0.0357
(1.00) 		0.626
(1.00) 		0.324
(1.00) 		0.0455
(1.00)
Del Peak 43(19q13 43) 0 (0%) 507 0.509
(1.00) 		0.816
(1.00) 		0.146
(1.00) 		0.3
(1.00) 		0.417
(1.00) 		0.44
(1.00) 		0.0156
(1.00) 		0.0712
(1.00) 		0.17
(1.00) 		0.289
(1.00) 		0.783
(1.00) 		0.0197
(1.00)
Del Peak 44(20p12 1) 0 (0%) 396 0.108
(1.00) 		0.631
(1.00) 		0.0445
(1.00) 		0.321
(1.00) 		0.144
(1.00) 		0.468
(1.00) 		0.319
(1.00) 		0.827
(1.00) 		0.191
(1.00) 		0.0632
(1.00) 		0.405
(1.00) 		0.829
(1.00)
Del Peak 45(20p12 1) 0 (0%) 396 0.108
(1.00) 		0.631
(1.00) 		0.0445
(1.00) 		0.321
(1.00) 		0.144
(1.00) 		0.468
(1.00) 		0.319
(1.00) 		0.827
(1.00) 		0.191
(1.00) 		0.0632
(1.00) 		0.405
(1.00) 		0.829
(1.00)
Del Peak 46(21q11 2) 0 (0%) 380 0.515
(1.00) 		0.721
(1.00) 		0.00555
(1.00) 		0.66
(1.00) 		0.000632
(0.529) 		0.824
(1.00) 		0.0458
(1.00) 		0.614
(1.00) 		0.325
(1.00) 		0.175
(1.00) 		0.433
(1.00) 		0.00411
(1.00)
Del Peak 47(22q13 32) 0 (0%) 371 0.04
(1.00) 		0.672
(1.00) 		0.173
(1.00) 		0.93
(1.00) 		0.00961
(1.00) 		0.45
(1.00) 		0.000791
(0.658) 		0.0275
(1.00) 		0.00938
(1.00) 		0.727
(1.00) 		0.293
(1.00) 		0.0122
(1.00)
'Amp Peak 5(6p21.1)' versus 'PATHOLOGY.N'

P value = 3.17e-05 (Fisher's exact test), Q value = 0.028

Table S1.  Gene #5: 'Amp Peak 5(6p21.1)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
AMP PEAK 5(6P21.1) CNV 63 39 43
AMP PEAK 5(6P21.1) WILD-TYPE 265 101 60

Figure S1.  Get High-res Image Gene #5: 'Amp Peak 5(6p21.1)' versus Clinical Feature #7: 'PATHOLOGY.N'

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

P value = 0.000225 (Fisher's exact test), Q value = 0.19

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 356 54 143 13
AMP PEAK 6(7P21.3) CNV 210 20 99 5
AMP PEAK 6(7P21.3) WILD-TYPE 146 34 44 8

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

'Amp Peak 6(7p21.3)' versus 'PATHOLOGY.N'

P value = 1.23e-05 (Fisher's exact test), Q value = 0.011

Table S3.  Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
AMP PEAK 6(7P21.3) CNV 164 100 69
AMP PEAK 6(7P21.3) WILD-TYPE 164 40 34

Figure S3.  Get High-res Image Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 6(7p21.3)' versus 'TUMOR.STAGE'

P value = 4.42e-06 (Fisher's exact test), Q value = 0.0039

Table S4.  Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
AMP PEAK 6(7P21.3) CNV 54 93 114 57
AMP PEAK 6(7P21.3) WILD-TYPE 43 114 52 24

Figure S4.  Get High-res Image Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 1.18e-09 (Fisher's exact test), Q value = 1.1e-06

Table S5.  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 356 54 143 13
AMP PEAK 14(13Q12.13) CNV 233 16 112 5
AMP PEAK 14(13Q12.13) WILD-TYPE 123 38 31 8

Figure S5.  Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 14(13q12.13)' versus 'PATHOLOGY.N'

P value = 3.88e-05 (Fisher's exact test), Q value = 0.034

Table S6.  Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
AMP PEAK 14(13Q12.13) CNV 186 105 77
AMP PEAK 14(13Q12.13) WILD-TYPE 142 35 26

Figure S6.  Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 14(13q12.13)' versus 'TUMOR.STAGE'

P value = 7.49e-05 (Fisher's exact test), Q value = 0.064

Table S7.  Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
AMP PEAK 14(13Q12.13) CNV 60 112 117 65
AMP PEAK 14(13Q12.13) WILD-TYPE 37 95 49 16

Figure S7.  Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 2.61e-09 (Fisher's exact test), Q value = 2.3e-06

Table S8.  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 356 54 143 13
AMP PEAK 15(13Q12.2) CNV 229 16 111 5
AMP PEAK 15(13Q12.2) WILD-TYPE 127 38 32 8

Figure S8.  Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 15(13q12.2)' versus 'PATHOLOGY.N'

P value = 9.03e-05 (Fisher's exact test), Q value = 0.077

Table S9.  Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
AMP PEAK 15(13Q12.2) CNV 184 103 76
AMP PEAK 15(13Q12.2) WILD-TYPE 144 37 27

Figure S9.  Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 15(13q12.2)' versus 'TUMOR.STAGE'

P value = 0.000184 (Fisher's exact test), Q value = 0.16

Table S10.  Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
AMP PEAK 15(13Q12.2) CNV 60 110 116 63
AMP PEAK 15(13Q12.2) WILD-TYPE 37 97 50 18

Figure S10.  Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 3.13e-08 (Fisher's exact test), Q value = 2.8e-05

Table S11.  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 356 54 143 13
AMP PEAK 16(13Q22.1) CNV 235 18 109 4
AMP PEAK 16(13Q22.1) WILD-TYPE 121 36 34 9

Figure S11.  Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 16(13q22.1)' versus 'PATHOLOGY.N'

P value = 0.000127 (Fisher's exact test), Q value = 0.11

Table S12.  Gene #16: 'Amp Peak 16(13q22.1)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
AMP PEAK 16(13Q22.1) CNV 187 105 75
AMP PEAK 16(13Q22.1) WILD-TYPE 141 35 28

Figure S12.  Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 18(16p11.2)' versus 'PATHOLOGY.N'

P value = 5.82e-05 (Fisher's exact test), Q value = 0.05

Table S13.  Gene #18: 'Amp Peak 18(16p11.2)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
AMP PEAK 18(16P11.2) CNV 68 52 39
AMP PEAK 18(16P11.2) WILD-TYPE 260 88 64

Figure S13.  Get High-res Image Gene #18: 'Amp Peak 18(16p11.2)' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 18(16p11.2)' versus 'TUMOR.STAGE'

P value = 8.54e-05 (Fisher's exact test), Q value = 0.073

Table S14.  Gene #18: 'Amp Peak 18(16p11.2)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
AMP PEAK 18(16P11.2) CNV 19 40 64 27
AMP PEAK 18(16P11.2) WILD-TYPE 78 167 102 54

Figure S14.  Get High-res Image Gene #18: 'Amp Peak 18(16p11.2)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 1.12e-05 (Fisher's exact test), Q value = 0.0098

Table S15.  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 356 54 143 13
AMP PEAK 24(20P11.21) CNV 207 20 103 4
AMP PEAK 24(20P11.21) WILD-TYPE 149 34 40 9

Figure S15.  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 = 0.008

Table S16.  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 S16.  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 = 7.88e-12 (Fisher's exact test), Q value = 7.1e-09

Table S17.  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 356 54 143 13
AMP PEAK 25(20Q11.21) CNV 269 24 132 7
AMP PEAK 25(20Q11.21) WILD-TYPE 87 30 11 6

Figure S17.  Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 25(20q11.21)' versus 'TUMOR.STAGE'

P value = 0.000107 (Fisher's exact test), Q value = 0.092

Table S18.  Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
AMP PEAK 25(20Q11.21) CNV 74 136 136 71
AMP PEAK 25(20Q11.21) WILD-TYPE 23 71 30 10

Figure S18.  Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 4.74e-06 (Fisher's exact test), Q value = 0.0042

Table S19.  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 S19.  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 = 5.38e-13 (Fisher's exact test), Q value = 4.8e-10

Table S20.  Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 143 13
AMP PEAK 26(20Q12) CNV 271 23 133 7
AMP PEAK 26(20Q12) WILD-TYPE 85 31 10 6

Figure S20.  Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 26(20q12)' versus 'TUMOR.STAGE'

P value = 4.17e-05 (Fisher's exact test), Q value = 0.036

Table S21.  Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
AMP PEAK 26(20Q12) CNV 74 137 135 73
AMP PEAK 26(20Q12) WILD-TYPE 23 70 31 8

Figure S21.  Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 2.18e-05 (Fisher's exact test), Q value = 0.019

Table S22.  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 S22.  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 = 8.76e-12 (Fisher's exact test), Q value = 7.8e-09

Table S23.  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 356 54 143 13
AMP PEAK 27(20Q13.32) CNV 273 24 132 7
AMP PEAK 27(20Q13.32) WILD-TYPE 83 30 11 6

Figure S23.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 27(20q13.32)' versus 'TUMOR.STAGE'

P value = 0.000131 (Fisher's exact test), Q value = 0.11

Table S24.  Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
AMP PEAK 27(20Q13.32) CNV 74 139 137 72
AMP PEAK 27(20Q13.32) WILD-TYPE 23 68 29 9

Figure S24.  Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 2.78e-05 (Fisher's exact test), Q value = 0.024

Table S25.  Gene #38: 'Del Peak 10(4p16.1)' versus Clinical Feature #10: '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 S25.  Get High-res Image Gene #38: 'Del Peak 10(4p16.1)' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

P value = 2.4e-05 (Fisher's exact test), Q value = 0.021

Table S26.  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 S26.  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 = 2.9e-05 (Fisher's exact test), Q value = 0.025

Table S27.  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 356 54 143 13
DEL PEAK 18(8P23.2) CNV 156 15 89 7
DEL PEAK 18(8P23.2) WILD-TYPE 200 39 54 6

Figure S27.  Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 18(8p23.2)' versus 'PATHOLOGY.N'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.024

Table S28.  Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
DEL PEAK 18(8P23.2) CNV 129 75 65
DEL PEAK 18(8P23.2) WILD-TYPE 199 65 38

Figure S28.  Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 18(8p23.2)' versus 'TUMOR.STAGE'

P value = 3.4e-05 (Fisher's exact test), Q value = 0.029

Table S29.  Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
DEL PEAK 18(8P23.2) CNV 39 78 92 52
DEL PEAK 18(8P23.2) WILD-TYPE 58 129 74 29

Figure S29.  Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 0.000256 (Fisher's exact test), Q value = 0.22

Table S30.  Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 143 13
DEL PEAK 19(8P22) CNV 168 16 89 7
DEL PEAK 19(8P22) WILD-TYPE 188 38 54 6

Figure S30.  Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 19(8p22)' versus 'PATHOLOGY.N'

P value = 1.97e-06 (Fisher's exact test), Q value = 0.0017

Table S31.  Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
DEL PEAK 19(8P22) CNV 134 78 70
DEL PEAK 19(8P22) WILD-TYPE 194 62 33

Figure S31.  Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 19(8p22)' versus 'TUMOR.STAGE'

P value = 1.24e-06 (Fisher's exact test), Q value = 0.0011

Table S32.  Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
DEL PEAK 19(8P22) CNV 39 81 99 55
DEL PEAK 19(8P22) WILD-TYPE 58 126 67 26

Figure S32.  Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 0.000106 (t-test), Q value = 0.091

Table S33.  Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 538 2.2 (4.8)
DEL PEAK 19(8P22) CNV 271 3.0 (5.7)
DEL PEAK 19(8P22) WILD-TYPE 267 1.4 (3.3)

Figure S33.  Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

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

P value = 1.15e-06 (Fisher's exact test), Q value = 0.001

Table S34.  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 356 54 143 13
DEL PEAK 30(14Q22.1) CNV 115 4 62 1
DEL PEAK 30(14Q22.1) WILD-TYPE 241 50 81 12

Figure S34.  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 = 4.34e-05 (logrank test), Q value = 0.037

Table S35.  Gene #62: 'Del Peak 34(16p13.3)' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 444 60 0.1 - 135.5 (7.0)
DEL PEAK 34(16P13.3) CNV 42 13 0.2 - 49.9 (7.6)
DEL PEAK 34(16P13.3) WILD-TYPE 402 47 0.1 - 135.5 (7.0)

Figure S35.  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 = 6.48e-08 (Fisher's exact test), Q value = 5.8e-05

Table S36.  Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 356 54 143 13
DEL PEAK 36(17P12) CNV 213 14 103 6
DEL PEAK 36(17P12) WILD-TYPE 143 40 40 7

Figure S36.  Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 36(17p12)' versus 'PATHOLOGY.N'

P value = 0.000121 (Fisher's exact test), Q value = 0.1

Table S37.  Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
DEL PEAK 36(17P12) CNV 171 95 74
DEL PEAK 36(17P12) WILD-TYPE 157 45 29

Figure S37.  Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 36(17p12)' versus 'TUMOR.STAGE'

P value = 3.15e-05 (Fisher's exact test), Q value = 0.027

Table S38.  Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
DEL PEAK 36(17P12) CNV 50 104 116 59
DEL PEAK 36(17P12) WILD-TYPE 47 103 50 22

Figure S38.  Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 1.82e-06 (Fisher's exact test), Q value = 0.0016

Table S39.  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 S39.  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 = 1.53e-16 (Fisher's exact test), Q value = 1.4e-13

Table S40.  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 356 54 143 13
DEL PEAK 38(18P11.31) CNV 211 7 113 6
DEL PEAK 38(18P11.31) WILD-TYPE 145 47 30 7

Figure S40.  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 = 1.4e-06

Table S41.  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 S41.  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 = 8.59e-18 (Fisher's exact test), Q value = 7.7e-15

Table S42.  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 356 54 143 13
DEL PEAK 39(18Q12.2) CNV 235 11 125 10
DEL PEAK 39(18Q12.2) WILD-TYPE 121 43 18 3

Figure S42.  Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 39(18q12.2)' versus 'PATHOLOGY.N'

P value = 0.000131 (Fisher's exact test), Q value = 0.11

Table S43.  Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
DEL PEAK 39(18Q12.2) CNV 196 107 79
DEL PEAK 39(18Q12.2) WILD-TYPE 132 33 24

Figure S43.  Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 39(18q12.2)' versus 'TUMOR.STAGE'

P value = 6.82e-05 (Fisher's exact test), Q value = 0.059

Table S44.  Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
DEL PEAK 39(18Q12.2) CNV 56 122 121 67
DEL PEAK 39(18Q12.2) WILD-TYPE 41 85 45 14

Figure S44.  Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 1.07e-09 (Fisher's exact test), Q value = 9.6e-07

Table S45.  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 S45.  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 = 3.7e-16 (Fisher's exact test), Q value = 3.3e-13

Table S46.  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 356 54 143 13
DEL PEAK 40(18Q21.2) CNV 245 14 126 12
DEL PEAK 40(18Q21.2) WILD-TYPE 111 40 17 1

Figure S46.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 40(18q21.2)' versus 'PATHOLOGY.N'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.0017

Table S47.  Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
DEL PEAK 40(18Q21.2) CNV 202 111 86
DEL PEAK 40(18Q21.2) WILD-TYPE 126 29 17

Figure S47.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 40(18q21.2)' versus 'TUMOR.STAGE'

P value = 4.1e-07 (Fisher's exact test), Q value = 0.00036

Table S48.  Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
DEL PEAK 40(18Q21.2) CNV 58 126 128 72
DEL PEAK 40(18Q21.2) WILD-TYPE 39 81 38 9

Figure S48.  Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #9: 'TUMOR.STAGE'

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

P value = 1.94e-07 (Fisher's exact test), Q value = 0.00017

Table S49.  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 S49.  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 = 2.07e-15 (Fisher's exact test), Q value = 1.9e-12

Table S50.  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 356 54 143 13
DEL PEAK 41(18Q22.1) CNV 246 13 124 10
DEL PEAK 41(18Q22.1) WILD-TYPE 110 41 19 3

Figure S50.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 41(18q22.1)' versus 'PATHOLOGY.N'

P value = 1.14e-05 (Fisher's exact test), Q value = 0.01

Table S51.  Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
DEL PEAK 41(18Q22.1) CNV 201 108 85
DEL PEAK 41(18Q22.1) WILD-TYPE 127 32 18

Figure S51.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 41(18q22.1)' versus 'TUMOR.STAGE'

P value = 4.68e-06 (Fisher's exact test), Q value = 0.0041

Table S52.  Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients I II III IV
ALL 97 207 166 81
DEL PEAK 41(18Q22.1) CNV 58 126 124 71
DEL PEAK 41(18Q22.1) WILD-TYPE 39 81 42 10

Figure S52.  Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 42(19p13.3)' versus 'PATHOLOGY.N'

P value = 7.64e-05 (Fisher's exact test), Q value = 0.066

Table S53.  Gene #70: 'Del Peak 42(19p13.3)' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 328 140 103
DEL PEAK 42(19P13.3) CNV 36 26 30
DEL PEAK 42(19P13.3) WILD-TYPE 292 114 73

Figure S53.  Get High-res Image Gene #70: 'Del Peak 42(19p13.3)' versus Clinical Feature #7: 'PATHOLOGY.N'

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)
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