Correlation between copy number variation genes (focal events) and selected clinical features
Colorectal Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C10C4TMC
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C10C4TMC
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 73 focal events and 13 clinical features across 604 patients, 73 significant findings detected with Q value < 0.25.

  • amp_6p21.1 cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • amp_7p21.3 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • amp_13q12.13 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • amp_13q12.2 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • amp_13q22.1 cnv correlated to 'PATHOLOGY.N.STAGE' and 'HISTOLOGICAL.TYPE'.

  • amp_16p11.2 cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • amp_20p11.21 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • amp_20q11.21 cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • amp_20q12 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE', and 'HISTOLOGICAL.TYPE'.

  • amp_20q13.31 cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

  • del_1p36.11 cnv correlated to 'PATHOLOGY.M.STAGE'.

  • del_4p16.2 cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION' and 'NUMBER.OF.LYMPH.NODES'.

  • del_4q22.1 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • del_4q35.1 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • del_5q12.1 cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

  • del_8p23.2 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • del_8p22 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • del_14q11.2 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_14q31.1 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_17p12 cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • del_17q24.3 cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • del_18p11.31 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.M.STAGE', and 'HISTOLOGICAL.TYPE'.

  • del_18q12.2 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • del_18q21.2 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'PATHOLOGY.M.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • del_18q22.1 cnv correlated to 'PRIMARY.SITE.OF.DISEASE',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.N.STAGE',  'PATHOLOGY.M.STAGE',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • del_19p13.3 cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • del_21q11.2 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_22q13.32 cnv correlated to 'PATHOLOGY.N.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 73 focal events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 73 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PRIMARY
SITE
OF
DISEASE 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		RACE
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test
del 18q21 2 425 (70%) 179 0.84
(1.00) 		0.0206
(1.00) 		3.46e-09
(3.28e-06) 		1e-05
(0.00937) 		0.317
(1.00) 		2e-05
(0.0183) 		0.00013
(0.115) 		0.109
(1.00) 		1e-05
(0.00937) 		0.0641
(1.00) 		0.0392
(1.00) 		1.61e-06
(0.00152) 		0.663
(1.00)
del 18q22 1 420 (70%) 184 0.955
(1.00) 		0.061
(1.00) 		1.6e-07
(0.000152) 		1e-05
(0.00937) 		0.453
(1.00) 		2e-05
(0.0183) 		0.00027
(0.237) 		0.132
(1.00) 		1e-05
(0.00937) 		0.0634
(1.00) 		0.078
(1.00) 		1.54e-05
(0.0142) 		0.365
(1.00)
del 8p23 2 284 (47%) 320 0.538
(1.00) 		0.146
(1.00) 		7.01e-05
(0.0631) 		5e-05
(0.0452) 		0.0769
(1.00) 		1e-05
(0.00937) 		0.00228
(1.00) 		0.034
(1.00) 		7e-05
(0.0631) 		0.0911
(1.00) 		0.0101
(1.00) 		3.56e-06
(0.00335) 		0.537
(1.00)
del 18q12 2 408 (68%) 196 0.957
(1.00) 		0.0136
(1.00) 		1.4e-09
(1.32e-06) 		0.00026
(0.229) 		0.343
(1.00) 		7e-05
(0.0631) 		0.0015
(1.00) 		0.297
(1.00) 		1e-05
(0.00937) 		0.0351
(1.00) 		0.0417
(1.00) 		0.000195
(0.173) 		0.39
(1.00)
amp 13q12 13 393 (65%) 211 0.293
(1.00) 		0.474
(1.00) 		0.000513
(0.441) 		3e-05
(0.0274) 		0.78
(1.00) 		2e-05
(0.0183) 		0.00168
(1.00) 		0.609
(1.00) 		1e-05
(0.00937) 		0.506
(1.00) 		0.0463
(1.00) 		7.11e-05
(0.0639) 		0.0181
(1.00)
amp 13q12 2 388 (64%) 216 0.405
(1.00) 		0.419
(1.00) 		0.000394
(0.343) 		6e-05
(0.0542) 		0.845
(1.00) 		2e-05
(0.0183) 		0.00636
(1.00) 		0.444
(1.00) 		1e-05
(0.00937) 		0.501
(1.00) 		0.0832
(1.00) 		8.9e-05
(0.0797) 		0.026
(1.00)
del 8p22 296 (49%) 308 0.11
(1.00) 		0.193
(1.00) 		0.000663
(0.567) 		1e-05
(0.00937) 		0.0234
(1.00) 		2e-05
(0.0183) 		0.00046
(0.398) 		0.122
(1.00) 		0.0001
(0.0892) 		0.101
(1.00) 		0.0065
(1.00) 		4.28e-08
(4.05e-05) 		0.259
(1.00)
del 17p12 361 (60%) 243 0.489
(1.00) 		0.145
(1.00) 		0.00197
(1.00) 		0.00023
(0.203) 		0.45
(1.00) 		6e-05
(0.0542) 		0.0199
(1.00) 		0.507
(1.00) 		1e-05
(0.00937) 		0.326
(1.00) 		0.155
(1.00) 		9.69e-06
(0.00909) 		0.767
(1.00)
del 18p11 31 363 (60%) 241 0.705
(1.00) 		0.00817
(1.00) 		2.45e-06
(0.00231) 		9e-05
(0.0805) 		0.896
(1.00) 		0.00829
(1.00) 		3e-05
(0.0274) 		0.74
(1.00) 		1e-05
(0.00937) 		0.328
(1.00) 		0.0207
(1.00) 		0.00908
(1.00) 		0.778
(1.00)
amp 7p21 3 357 (59%) 247 0.625
(1.00) 		0.0449
(1.00) 		0.0248
(1.00) 		8e-05
(0.0718) 		0.931
(1.00) 		1e-05
(0.00937) 		0.052
(1.00) 		1
(1.00) 		0.00104
(0.887) 		0.0898
(1.00) 		0.295
(1.00) 		3.5e-05
(0.0317) 		0.597
(1.00)
amp 20q12 461 (76%) 143 0.706
(1.00) 		0.508
(1.00) 		1.51e-06
(0.00143) 		0.00024
(0.212) 		0.355
(1.00) 		0.00035
(0.307) 		0.00276
(1.00) 		0.252
(1.00) 		1e-05
(0.00937) 		0.693
(1.00) 		0.0387
(1.00) 		0.00279
(1.00) 		0.161
(1.00)
amp 6p21 1 152 (25%) 452 0.644
(1.00) 		0.819
(1.00) 		0.0254
(1.00) 		0.0131
(1.00) 		0.239
(1.00) 		0.00013
(0.115) 		0.059
(1.00) 		0.133
(1.00) 		0.00438
(1.00) 		0.00129
(1.00) 		0.113
(1.00) 		0.000262
(0.23) 		0.151
(1.00)
amp 13q22 1 391 (65%) 213 0.427
(1.00) 		0.7
(1.00) 		0.0165
(1.00) 		0.00059
(0.506) 		0.739
(1.00) 		3e-05
(0.0274) 		0.00916
(1.00) 		0.173
(1.00) 		1e-05
(0.00937) 		0.504
(1.00) 		0.256
(1.00) 		0.000406
(0.354) 		0.0969
(1.00)
amp 16p11 2 169 (28%) 435 0.806
(1.00) 		0.288
(1.00) 		0.759
(1.00) 		0.00042
(0.365) 		0.718
(1.00) 		3e-05
(0.0274) 		0.176
(1.00) 		0.928
(1.00) 		0.00247
(1.00) 		0.275
(1.00) 		0.278
(1.00) 		3.32e-05
(0.0301) 		0.559
(1.00)
amp 20q11 21 459 (76%) 145 0.58
(1.00) 		0.603
(1.00) 		2.99e-06
(0.00282) 		0.00076
(0.649) 		0.265
(1.00) 		0.00051
(0.439) 		0.0184
(1.00) 		0.254
(1.00) 		1e-05
(0.00937) 		0.694
(1.00) 		0.0397
(1.00) 		0.00267
(1.00) 		0.278
(1.00)
amp 20q13 31 464 (77%) 140 0.655
(1.00) 		0.54
(1.00) 		2.4e-06
(0.00226) 		0.00041
(0.356) 		0.224
(1.00) 		0.00046
(0.398) 		0.0036
(1.00) 		0.44
(1.00) 		1e-05
(0.00937) 		0.692
(1.00) 		0.0396
(1.00) 		0.00252
(1.00) 		0.157
(1.00)
del 4p16 2 193 (32%) 411 0.124
(1.00) 		0.895
(1.00) 		0.0481
(1.00) 		0.00272
(1.00) 		0.823
(1.00) 		0.00047
(0.406) 		0.00237
(1.00) 		0.162
(1.00) 		0.0177
(1.00) 		3.05e-05
(0.0277) 		0.0923
(1.00) 		9.72e-05
(0.0868) 		0.37
(1.00)
del 19p13 3 95 (16%) 509 0.277
(1.00) 		0.254
(1.00) 		0.0584
(1.00) 		0.00676
(1.00) 		0.399
(1.00) 		0.0001
(0.0892) 		0.028
(1.00) 		0.37
(1.00) 		0.0891
(1.00) 		0.638
(1.00) 		0.147
(1.00) 		4.71e-06
(0.00443) 		0.873
(1.00)
del 22q13 32 222 (37%) 382 0.026
(1.00) 		0.96
(1.00) 		0.214
(1.00) 		0.014
(1.00) 		0.369
(1.00) 		0.00028
(0.246) 		0.0258
(1.00) 		0.399
(1.00) 		0.00396
(1.00) 		0.731
(1.00) 		0.402
(1.00) 		0.000266
(0.234) 		0.643
(1.00)
amp 20p11 21 355 (59%) 249 0.508
(1.00) 		0.708
(1.00) 		0.00669
(1.00) 		0.0125
(1.00) 		0.777
(1.00) 		0.363
(1.00) 		0.00576
(1.00) 		0.0684
(1.00) 		1e-05
(0.00937) 		0.319
(1.00) 		0.402
(1.00) 		0.66
(1.00) 		0.482
(1.00)
del 1p36 11 239 (40%) 365 0.0943
(1.00) 		0.0466
(1.00) 		0.0903
(1.00) 		0.00343
(1.00) 		0.31
(1.00) 		0.00368
(1.00) 		0.00012
(0.107) 		0.211
(1.00) 		0.0022
(1.00) 		0.745
(1.00) 		0.0856
(1.00) 		0.000352
(0.308) 		0.328
(1.00)
del 4q22 1 215 (36%) 389 0.33
(1.00) 		0.157
(1.00) 		0.0159
(1.00) 		0.0268
(1.00) 		0.136
(1.00) 		0.00038
(0.332) 		0.464
(1.00) 		0.106
(1.00) 		0.00163
(1.00) 		0.00147
(1.00) 		0.792
(1.00) 		0.000108
(0.0959) 		0.818
(1.00)
del 4q35 1 224 (37%) 380 0.898
(1.00) 		0.102
(1.00) 		0.0705
(1.00) 		0.058
(1.00) 		0.589
(1.00) 		0.00105
(0.895) 		0.361
(1.00) 		1
(1.00) 		0.0441
(1.00) 		0.00202
(1.00) 		0.765
(1.00) 		0.000206
(0.182) 		0.558
(1.00)
del 5q12 1 153 (25%) 451 0.167
(1.00) 		0.119
(1.00) 		0.0154
(1.00) 		0.0274
(1.00) 		0.995
(1.00) 		0.00876
(1.00) 		0.00957
(1.00) 		0.513
(1.00) 		0.00998
(1.00) 		0.000104
(0.0926) 		0.642
(1.00) 		0.00515
(1.00) 		0.403
(1.00)
del 14q11 2 206 (34%) 398 0.551
(1.00) 		0.216
(1.00) 		0.0116
(1.00) 		0.792
(1.00) 		0.298
(1.00) 		0.0487
(1.00) 		0.199
(1.00) 		1
(1.00) 		1e-05
(0.00937) 		0.499
(1.00) 		0.875
(1.00) 		0.144
(1.00) 		1
(1.00)
del 14q31 1 212 (35%) 392 0.974
(1.00) 		0.106
(1.00) 		0.0339
(1.00) 		0.576
(1.00) 		0.208
(1.00) 		0.0395
(1.00) 		0.0427
(1.00) 		0.393
(1.00) 		1e-05
(0.00937) 		0.505
(1.00) 		0.737
(1.00) 		0.0394
(1.00) 		0.981
(1.00)
del 17q24 3 94 (16%) 510 0.0832
(1.00) 		0.184
(1.00) 		1
(1.00) 		0.00928
(1.00) 		0.0962
(1.00) 		0.00188
(1.00) 		0.00194
(1.00) 		0.179
(1.00) 		0.978
(1.00) 		0.636
(1.00) 		0.388
(1.00) 		5.44e-05
(0.0492) 		0.172
(1.00)
del 21q11 2 209 (35%) 395 0.349
(1.00) 		0.698
(1.00) 		0.00362
(1.00) 		0.427
(1.00) 		0.934
(1.00) 		0.0731
(1.00) 		0.5
(1.00) 		0.668
(1.00) 		8e-05
(0.0718) 		0.288
(1.00) 		0.608
(1.00) 		0.0138
(1.00) 		0.503
(1.00)
amp 1q31 1 143 (24%) 461 0.619
(1.00) 		0.234
(1.00) 		0.0649
(1.00) 		0.327
(1.00) 		0.315
(1.00) 		0.0563
(1.00) 		0.185
(1.00) 		0.212
(1.00) 		0.149
(1.00) 		0.0382
(1.00) 		0.728
(1.00) 		0.00948
(1.00) 		0.949
(1.00)
amp 2q33 1 137 (23%) 467 0.0831
(1.00) 		0.924
(1.00) 		0.0115
(1.00) 		0.0376
(1.00) 		0.894
(1.00) 		0.00178
(1.00) 		0.177
(1.00) 		0.923
(1.00) 		0.00107
(0.911) 		0.124
(1.00) 		0.383
(1.00) 		0.00264
(1.00) 		0.236
(1.00)
amp 5p12 116 (19%) 488 0.092
(1.00) 		0.148
(1.00) 		0.048
(1.00) 		0.283
(1.00) 		0.466
(1.00) 		0.0432
(1.00) 		0.203
(1.00) 		0.679
(1.00) 		0.016
(1.00) 		0.385
(1.00) 		0.0571
(1.00) 		0.00979
(1.00) 		0.58
(1.00)
amp 5q22 3 63 (10%) 541 0.274
(1.00) 		0.856
(1.00) 		0.371
(1.00) 		0.605
(1.00) 		0.961
(1.00) 		0.31
(1.00) 		0.084
(1.00) 		0.895
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.0572
(1.00) 		0.182
(1.00) 		0.606
(1.00)
amp 8p11 23 208 (34%) 396 0.376
(1.00) 		0.802
(1.00) 		0.563
(1.00) 		0.299
(1.00) 		0.554
(1.00) 		0.541
(1.00) 		0.258
(1.00) 		0.607
(1.00) 		0.247
(1.00) 		0.503
(1.00) 		0.0816
(1.00) 		0.835
(1.00) 		0.795
(1.00)
amp 8p11 21 252 (42%) 352 0.634
(1.00) 		0.478
(1.00) 		0.78
(1.00) 		0.125
(1.00) 		0.507
(1.00) 		0.389
(1.00) 		0.16
(1.00) 		0.187
(1.00) 		0.196
(1.00) 		0.741
(1.00) 		0.0252
(1.00) 		0.561
(1.00) 		0.642
(1.00)
amp 8q12 1 325 (54%) 279 0.669
(1.00) 		0.104
(1.00) 		0.357
(1.00) 		0.0674
(1.00) 		0.334
(1.00) 		0.103
(1.00) 		0.0111
(1.00) 		0.414
(1.00) 		0.016
(1.00) 		0.0425
(1.00) 		0.0905
(1.00) 		0.117
(1.00) 		0.454
(1.00)
amp 8q24 21 362 (60%) 242 0.383
(1.00) 		0.166
(1.00) 		0.0753
(1.00) 		0.0826
(1.00) 		0.286
(1.00) 		0.149
(1.00) 		0.0229
(1.00) 		0.213
(1.00) 		0.0129
(1.00) 		0.093
(1.00) 		0.194
(1.00) 		0.207
(1.00) 		0.64
(1.00)
amp 10q22 3 38 (6%) 566 0.941
(1.00) 		0.267
(1.00) 		0.85
(1.00) 		0.577
(1.00) 		0.193
(1.00) 		0.0443
(1.00) 		0.76
(1.00) 		0.616
(1.00) 		0.903
(1.00) 		0.445
(1.00) 		0.928
(1.00) 		0.0624
(1.00) 		0.912
(1.00)
amp 11p15 5 135 (22%) 469 0.752
(1.00) 		0.0368
(1.00) 		0.0773
(1.00) 		0.867
(1.00) 		0.287
(1.00) 		0.365
(1.00) 		0.286
(1.00) 		0.769
(1.00) 		0.00047
(0.406) 		0.118
(1.00) 		0.844
(1.00) 		0.326
(1.00) 		0.554
(1.00)
amp 12p13 32 149 (25%) 455 0.233
(1.00) 		0.165
(1.00) 		0.749
(1.00) 		0.0836
(1.00) 		0.377
(1.00) 		0.0971
(1.00) 		0.121
(1.00) 		0.777
(1.00) 		0.508
(1.00) 		0.696
(1.00) 		0.752
(1.00) 		0.355
(1.00) 		0.697
(1.00)
amp 15q26 1 42 (7%) 562 0.304
(1.00) 		0.781
(1.00) 		0.589
(1.00) 		0.14
(1.00) 		0.337
(1.00) 		0.0023
(1.00) 		0.569
(1.00) 		0.2
(1.00) 		0.533
(1.00) 		0.125
(1.00) 		0.494
(1.00) 		0.00375
(1.00) 		0.714
(1.00)
amp 17q12 157 (26%) 447 0.0562
(1.00) 		0.169
(1.00) 		0.465
(1.00) 		0.304
(1.00) 		0.297
(1.00) 		0.156
(1.00) 		0.00993
(1.00) 		0.115
(1.00) 		0.318
(1.00) 		0.458
(1.00) 		0.0462
(1.00) 		0.248
(1.00) 		0.178
(1.00)
amp 17q24 1 140 (23%) 464 0.0105
(1.00) 		0.241
(1.00) 		0.914
(1.00) 		0.745
(1.00) 		0.788
(1.00) 		0.983
(1.00) 		0.0807
(1.00) 		0.562
(1.00) 		0.0639
(1.00) 		0.692
(1.00) 		0.106
(1.00) 		0.632
(1.00) 		0.851
(1.00)
amp 19p13 2 109 (18%) 495 0.673
(1.00) 		0.707
(1.00) 		0.122
(1.00) 		0.739
(1.00) 		0.404
(1.00) 		0.0846
(1.00) 		0.276
(1.00) 		0.205
(1.00) 		0.0353
(1.00) 		1
(1.00) 		0.114
(1.00) 		0.467
(1.00) 		0.541
(1.00)
amp 19q12 136 (23%) 468 0.661
(1.00) 		0.468
(1.00) 		0.124
(1.00) 		0.51
(1.00) 		0.833
(1.00) 		0.105
(1.00) 		0.0544
(1.00) 		0.205
(1.00) 		0.0136
(1.00) 		1
(1.00) 		0.414
(1.00) 		0.275
(1.00) 		0.734
(1.00)
amp 20p12 1 274 (45%) 330 0.28
(1.00) 		0.494
(1.00) 		0.166
(1.00) 		0.003
(1.00) 		0.896
(1.00) 		0.127
(1.00) 		0.00147
(1.00) 		0.0332
(1.00) 		0.0078
(1.00) 		0.0866
(1.00) 		0.0674
(1.00) 		0.134
(1.00) 		0.71
(1.00)
del 1p33 172 (28%) 432 0.0596
(1.00) 		0.6
(1.00) 		0.309
(1.00) 		0.0348
(1.00) 		0.32
(1.00) 		0.0224
(1.00) 		0.0312
(1.00) 		0.653
(1.00) 		0.0341
(1.00) 		0.719
(1.00) 		0.286
(1.00) 		0.00539
(1.00) 		0.27
(1.00)
del 1p13 2 171 (28%) 433 0.0609
(1.00) 		0.753
(1.00) 		0.22
(1.00) 		0.00726
(1.00) 		0.186
(1.00) 		0.00636
(1.00) 		0.00598
(1.00) 		0.588
(1.00) 		0.082
(1.00) 		0.28
(1.00) 		0.353
(1.00) 		0.000483
(0.416) 		0.448
(1.00)
del 2p12 21 (3%) 583 0.991
(1.00) 		0.128
(1.00) 		0.000669
(0.572) 		0.407
(1.00) 		1
(1.00) 		0.443
(1.00) 		0.351
(1.00) 		0.66
(1.00) 		0.00613
(1.00) 		0.274
(1.00) 		0.885
(1.00) 		0.399
(1.00) 		0.676
(1.00)
del 2q22 1 35 (6%) 569 0.823
(1.00) 		0.836
(1.00) 		0.558
(1.00) 		0.325
(1.00) 		0.637
(1.00) 		0.505
(1.00) 		0.418
(1.00) 		0.728
(1.00) 		0.906
(1.00) 		1
(1.00) 		0.931
(1.00) 		0.239
(1.00) 		0.0123
(1.00)
del 3p26 3 90 (15%) 514 0.0737
(1.00) 		0.453
(1.00) 		0.365
(1.00) 		0.0332
(1.00) 		0.0891
(1.00) 		0.00888
(1.00) 		0.00531
(1.00) 		0.648
(1.00) 		0.061
(1.00) 		0.629
(1.00) 		0.0668
(1.00) 		0.0053
(1.00) 		0.601
(1.00)
del 3p14 2 116 (19%) 488 0.331
(1.00) 		0.241
(1.00) 		0.726
(1.00) 		0.225
(1.00) 		0.106
(1.00) 		0.208
(1.00) 		0.0948
(1.00) 		0.535
(1.00) 		0.721
(1.00) 		0.685
(1.00) 		0.297
(1.00) 		0.0891
(1.00) 		0.504
(1.00)
del 3q26 31 62 (10%) 542 0.43
(1.00) 		0.808
(1.00) 		0.88
(1.00) 		0.0349
(1.00) 		0.102
(1.00) 		0.0941
(1.00) 		0.152
(1.00) 		0.424
(1.00) 		0.00928
(1.00) 		1
(1.00) 		0.818
(1.00) 		0.159
(1.00) 		0.633
(1.00)
del 5q21 2 182 (30%) 422 0.119
(1.00) 		0.144
(1.00) 		0.271
(1.00) 		0.00582
(1.00) 		0.754
(1.00) 		0.00038
(0.332) 		0.0171
(1.00) 		0.859
(1.00) 		0.0564
(1.00) 		0.000406
(0.354) 		0.619
(1.00) 		0.000521
(0.448) 		0.577
(1.00)
del 5q22 2 184 (30%) 420 0.0947
(1.00) 		0.387
(1.00) 		0.0726
(1.00) 		0.0345
(1.00) 		0.735
(1.00) 		0.0117
(1.00) 		0.0175
(1.00) 		0.376
(1.00) 		0.0392
(1.00) 		0.000442
(0.383) 		0.268
(1.00) 		0.00946
(1.00) 		0.543
(1.00)
del 6p25 3 78 (13%) 526 0.0765
(1.00) 		0.0621
(1.00) 		0.889
(1.00) 		0.458
(1.00) 		0.473
(1.00) 		0.493
(1.00) 		0.396
(1.00) 		0.0694
(1.00) 		0.49
(1.00) 		0.328
(1.00) 		0.46
(1.00) 		0.455
(1.00) 		0.0051
(1.00)
del 6q26 91 (15%) 513 0.0176
(1.00) 		0.708
(1.00) 		0.303
(1.00) 		0.188
(1.00) 		0.163
(1.00) 		0.00301
(1.00) 		0.107
(1.00) 		0.211
(1.00) 		0.0397
(1.00) 		0.631
(1.00) 		0.184
(1.00) 		0.00225
(1.00) 		0.0235
(1.00)
del 7q31 1 16 (3%) 588 0.989
(1.00) 		0.557
(1.00) 		1
(1.00) 		0.723
(1.00) 		0.493
(1.00) 		0.939
(1.00) 		0.113
(1.00) 		0.46
(1.00) 		0.489
(1.00) 		1
(1.00) 		0.634
(1.00) 		0.698
(1.00) 		0.57
(1.00)
del 8q11 1 47 (8%) 557 0.381
(1.00) 		0.309
(1.00) 		0.228
(1.00) 		0.154
(1.00) 		0.681
(1.00) 		0.0555
(1.00) 		0.0434
(1.00) 		0.228
(1.00) 		0.564
(1.00) 		0.52
(1.00) 		0.322
(1.00) 		0.0271
(1.00) 		0.0747
(1.00)
del 9p24 2 82 (14%) 522 0.345
(1.00) 		0.106
(1.00) 		0.283
(1.00) 		0.78
(1.00) 		0.437
(1.00) 		0.122
(1.00) 		0.115
(1.00) 		0.0564
(1.00) 		0.119
(1.00) 		0.351
(1.00) 		0.137
(1.00) 		0.0332
(1.00) 		0.719
(1.00)
del 10p15 3 112 (19%) 492 0.483
(1.00) 		0.0322
(1.00) 		0.345
(1.00) 		0.0399
(1.00) 		0.619
(1.00) 		0.0198
(1.00) 		0.114
(1.00) 		0.834
(1.00) 		0.419
(1.00) 		0.0135
(1.00) 		0.867
(1.00) 		0.00396
(1.00) 		0.71
(1.00)
del 10q21 1 135 (22%) 469 0.692
(1.00) 		0.0327
(1.00) 		0.44
(1.00) 		0.0892
(1.00) 		0.92
(1.00) 		0.0709
(1.00) 		0.366
(1.00) 		0.845
(1.00) 		0.0409
(1.00) 		0.0301
(1.00) 		0.273
(1.00) 		0.0244
(1.00) 		0.686
(1.00)
del 10q23 31 157 (26%) 447 0.506
(1.00) 		0.00482
(1.00) 		0.0745
(1.00) 		0.0435
(1.00) 		0.59
(1.00) 		0.0556
(1.00) 		0.0577
(1.00) 		1
(1.00) 		0.0127
(1.00) 		0.0116
(1.00) 		0.699
(1.00) 		0.0144
(1.00) 		0.91
(1.00)
del 10q25 2 154 (25%) 450 0.371
(1.00) 		0.0409
(1.00) 		0.246
(1.00) 		0.171
(1.00) 		0.308
(1.00) 		0.0193
(1.00) 		0.318
(1.00) 		0.926
(1.00) 		0.034
(1.00) 		0.0105
(1.00) 		0.676
(1.00) 		0.0132
(1.00) 		1
(1.00)
del 11q22 3 109 (18%) 495 0.297
(1.00) 		0.48
(1.00) 		0.07
(1.00) 		0.682
(1.00) 		0.674
(1.00) 		0.193
(1.00) 		0.368
(1.00) 		0.751
(1.00) 		0.0416
(1.00) 		0.21
(1.00) 		0.55
(1.00) 		0.0526
(1.00) 		0.252
(1.00)
del 12p13 1 89 (15%) 515 0.0474
(1.00) 		0.215
(1.00) 		0.149
(1.00) 		0.232
(1.00) 		0.547
(1.00) 		0.0295
(1.00) 		0.0759
(1.00) 		0.818
(1.00) 		0.0175
(1.00) 		0.628
(1.00) 		0.902
(1.00) 		0.0952
(1.00) 		0.925
(1.00)
del 12q21 33 88 (15%) 516 0.134
(1.00) 		0.869
(1.00) 		0.363
(1.00) 		0.0663
(1.00) 		0.637
(1.00) 		0.0705
(1.00) 		0.451
(1.00) 		0.645
(1.00) 		0.031
(1.00) 		0.626
(1.00) 		0.548
(1.00) 		0.0191
(1.00) 		0.961
(1.00)
del 15q11 2 246 (41%) 358 0.89
(1.00) 		0.337
(1.00) 		0.134
(1.00) 		0.0741
(1.00) 		0.766
(1.00) 		0.0127
(1.00) 		0.0846
(1.00) 		0.407
(1.00) 		0.0497
(1.00) 		0.0356
(1.00) 		0.829
(1.00) 		0.00382
(1.00) 		0.195
(1.00)
del 15q15 2 243 (40%) 361 0.984
(1.00) 		0.202
(1.00) 		0.0244
(1.00) 		0.0507
(1.00) 		0.759
(1.00) 		0.00297
(1.00) 		0.0237
(1.00) 		0.28
(1.00) 		0.0122
(1.00) 		0.0344
(1.00) 		0.531
(1.00) 		0.00186
(1.00) 		0.122
(1.00)
del 15q21 1 241 (40%) 363 0.621
(1.00) 		0.424
(1.00) 		0.024
(1.00) 		0.122
(1.00) 		0.815
(1.00) 		0.0161
(1.00) 		0.0374
(1.00) 		0.212
(1.00) 		0.0122
(1.00) 		0.0336
(1.00) 		0.447
(1.00) 		0.00846
(1.00) 		0.0624
(1.00)
del 15q22 33 231 (38%) 373 0.881
(1.00) 		0.268
(1.00) 		0.0136
(1.00) 		0.00794
(1.00) 		0.0794
(1.00) 		0.00169
(1.00) 		0.0396
(1.00) 		0.402
(1.00) 		0.0074
(1.00) 		0.00255
(1.00) 		0.58
(1.00) 		0.000652
(0.559) 		0.0468
(1.00)
del 16p13 3 67 (11%) 537 0.00137
(1.00) 		0.772
(1.00) 		0.147
(1.00) 		0.0117
(1.00) 		0.0605
(1.00) 		0.184
(1.00) 		0.275
(1.00) 		0.795
(1.00) 		0.227
(1.00) 		0.607
(1.00) 		0.438
(1.00) 		0.128
(1.00) 		0.256
(1.00)
del 16q23 1 81 (13%) 523 0.0102
(1.00) 		0.671
(1.00) 		0.788
(1.00) 		0.349
(1.00) 		0.188
(1.00) 		0.55
(1.00) 		0.463
(1.00) 		0.341
(1.00) 		0.774
(1.00) 		1
(1.00) 		0.891
(1.00) 		0.971
(1.00) 		0.3
(1.00)
del 20p12 1 132 (22%) 472 0.689
(1.00) 		0.342
(1.00) 		0.00732
(1.00) 		0.129
(1.00) 		0.765
(1.00) 		0.178
(1.00) 		0.801
(1.00) 		0.555
(1.00) 		0.00472
(1.00) 		0.217
(1.00) 		0.563
(1.00) 		0.0606
(1.00) 		0.237
(1.00)
'amp_6p21.1' versus 'PATHOLOGY.N.STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.12

Table S1.  Gene #5: 'amp_6p21.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
AMP PEAK 5(6P21.1) MUTATED 66 41 44
AMP PEAK 5(6P21.1) WILD-TYPE 275 107 68

Figure S1.  Get High-res Image Gene #5: 'amp_6p21.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_6p21.1' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000262 (Wilcoxon-test), Q value = 0.23

Table S2.  Gene #5: 'amp_6p21.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
AMP PEAK 5(6P21.1) MUTATED 146 3.4 (6.0)
AMP PEAK 5(6P21.1) WILD-TYPE 424 1.8 (4.1)

Figure S2.  Get High-res Image Gene #5: 'amp_6p21.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'amp_7p21.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.072

Table S3.  Gene #6: 'amp_7p21.3' versus Clinical Feature #4: '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 102 1 36 171 10 3 26 21 78 53 61 27 2
AMP PEAK 6(7P21.3) MUTATED 56 1 19 77 3 2 15 15 58 38 42 21 1
AMP PEAK 6(7P21.3) WILD-TYPE 46 0 17 94 7 1 11 6 20 15 19 6 1

Figure S3.  Get High-res Image Gene #6: 'amp_7p21.3' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'amp_7p21.3' versus 'PATHOLOGY.N.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S4.  Gene #6: 'amp_7p21.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
AMP PEAK 6(7P21.3) MUTATED 170 107 77
AMP PEAK 6(7P21.3) WILD-TYPE 171 41 35

Figure S4.  Get High-res Image Gene #6: 'amp_7p21.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_7p21.3' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.5e-05 (Wilcoxon-test), Q value = 0.032

Table S5.  Gene #6: 'amp_7p21.3' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
AMP PEAK 6(7P21.3) MUTATED 339 2.6 (5.1)
AMP PEAK 6(7P21.3) WILD-TYPE 231 1.7 (4.0)

Figure S5.  Get High-res Image Gene #6: 'amp_7p21.3' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'amp_13q12.13' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.027

Table S6.  Gene #14: 'amp_13q12.13' versus Clinical Feature #4: '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 102 1 36 171 10 3 26 21 78 53 61 27 2
AMP PEAK 14(13Q12.13) MUTATED 63 0 16 98 4 3 15 17 58 38 50 23 0
AMP PEAK 14(13Q12.13) WILD-TYPE 39 1 20 73 6 0 11 4 20 15 11 4 2

Figure S6.  Get High-res Image Gene #14: 'amp_13q12.13' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'amp_13q12.13' versus 'PATHOLOGY.N.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S7.  Gene #14: 'amp_13q12.13' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
AMP PEAK 14(13Q12.13) MUTATED 194 112 85
AMP PEAK 14(13Q12.13) WILD-TYPE 147 36 27

Figure S7.  Get High-res Image Gene #14: 'amp_13q12.13' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_13q12.13' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S8.  Gene #14: 'amp_13q12.13' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
AMP PEAK 14(13Q12.13) MUTATED 249 17 117 5
AMP PEAK 14(13Q12.13) WILD-TYPE 129 42 29 8

Figure S8.  Get High-res Image Gene #14: 'amp_13q12.13' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'amp_13q12.13' versus 'NUMBER.OF.LYMPH.NODES'

P value = 7.11e-05 (Wilcoxon-test), Q value = 0.064

Table S9.  Gene #14: 'amp_13q12.13' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
AMP PEAK 14(13Q12.13) MUTATED 375 2.5 (4.9)
AMP PEAK 14(13Q12.13) WILD-TYPE 195 1.6 (4.2)

Figure S9.  Get High-res Image Gene #14: 'amp_13q12.13' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'amp_13q12.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.054

Table S10.  Gene #15: 'amp_13q12.2' versus Clinical Feature #4: '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 102 1 36 171 10 3 26 21 78 53 61 27 2
AMP PEAK 15(13Q12.2) MUTATED 63 0 16 96 4 3 15 17 58 37 49 22 0
AMP PEAK 15(13Q12.2) WILD-TYPE 39 1 20 75 6 0 11 4 20 16 12 5 2

Figure S10.  Get High-res Image Gene #15: 'amp_13q12.2' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'amp_13q12.2' versus 'PATHOLOGY.N.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S11.  Gene #15: 'amp_13q12.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
AMP PEAK 15(13Q12.2) MUTATED 192 110 84
AMP PEAK 15(13Q12.2) WILD-TYPE 149 38 28

Figure S11.  Get High-res Image Gene #15: 'amp_13q12.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_13q12.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S12.  Gene #15: 'amp_13q12.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
AMP PEAK 15(13Q12.2) MUTATED 245 17 116 5
AMP PEAK 15(13Q12.2) WILD-TYPE 133 42 30 8

Figure S12.  Get High-res Image Gene #15: 'amp_13q12.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'amp_13q12.2' versus 'NUMBER.OF.LYMPH.NODES'

P value = 8.9e-05 (Wilcoxon-test), Q value = 0.08

Table S13.  Gene #15: 'amp_13q12.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
AMP PEAK 15(13Q12.2) MUTATED 371 2.5 (4.9)
AMP PEAK 15(13Q12.2) WILD-TYPE 199 1.6 (4.2)

Figure S13.  Get High-res Image Gene #15: 'amp_13q12.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'amp_13q22.1' versus 'PATHOLOGY.N.STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.027

Table S14.  Gene #16: 'amp_13q22.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
AMP PEAK 16(13Q22.1) MUTATED 194 111 83
AMP PEAK 16(13Q22.1) WILD-TYPE 147 37 29

Figure S14.  Get High-res Image Gene #16: 'amp_13q22.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_13q22.1' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S15.  Gene #16: 'amp_13q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
AMP PEAK 16(13Q22.1) MUTATED 251 19 112 4
AMP PEAK 16(13Q22.1) WILD-TYPE 127 40 34 9

Figure S15.  Get High-res Image Gene #16: 'amp_13q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'amp_16p11.2' versus 'PATHOLOGY.N.STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.027

Table S16.  Gene #18: 'amp_16p11.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
AMP PEAK 18(16P11.2) MUTATED 70 55 43
AMP PEAK 18(16P11.2) WILD-TYPE 271 93 69

Figure S16.  Get High-res Image Gene #18: 'amp_16p11.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'amp_16p11.2' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.32e-05 (Wilcoxon-test), Q value = 0.03

Table S17.  Gene #18: 'amp_16p11.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
AMP PEAK 18(16P11.2) MUTATED 161 3.1 (5.9)
AMP PEAK 18(16P11.2) WILD-TYPE 409 1.9 (4.1)

Figure S17.  Get High-res Image Gene #18: 'amp_16p11.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'amp_20p11.21' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S18.  Gene #24: 'amp_20p11.21' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
AMP PEAK 24(20P11.21) MUTATED 221 21 105 4
AMP PEAK 24(20P11.21) WILD-TYPE 157 38 41 9

Figure S18.  Get High-res Image Gene #24: 'amp_20p11.21' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'amp_20q11.21' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.99e-06 (Fisher's exact test), Q value = 0.0028

Table S19.  Gene #25: 'amp_20q11.21' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 438 162
AMP PEAK 25(20Q11.21) MUTATED 312 144
AMP PEAK 25(20Q11.21) WILD-TYPE 126 18

Figure S19.  Get High-res Image Gene #25: 'amp_20q11.21' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'amp_20q11.21' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S20.  Gene #25: 'amp_20q11.21' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
AMP PEAK 25(20Q11.21) MUTATED 286 25 135 7
AMP PEAK 25(20Q11.21) WILD-TYPE 92 34 11 6

Figure S20.  Get High-res Image Gene #25: 'amp_20q11.21' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'amp_20q12' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.51e-06 (Fisher's exact test), Q value = 0.0014

Table S21.  Gene #26: 'amp_20q12' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 438 162
AMP PEAK 26(20Q12) MUTATED 313 145
AMP PEAK 26(20Q12) WILD-TYPE 125 17

Figure S21.  Get High-res Image Gene #26: 'amp_20q12' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'amp_20q12' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00024 (Fisher's exact test), Q value = 0.21

Table S22.  Gene #26: 'amp_20q12' versus Clinical Feature #4: '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 102 1 36 171 10 3 26 21 78 53 61 27 2
AMP PEAK 26(20Q12) MUTATED 77 1 21 118 5 3 18 20 62 44 55 25 1
AMP PEAK 26(20Q12) WILD-TYPE 25 0 15 53 5 0 8 1 16 9 6 2 1

Figure S22.  Get High-res Image Gene #26: 'amp_20q12' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'amp_20q12' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S23.  Gene #26: 'amp_20q12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
AMP PEAK 26(20Q12) MUTATED 288 24 136 7
AMP PEAK 26(20Q12) WILD-TYPE 90 35 10 6

Figure S23.  Get High-res Image Gene #26: 'amp_20q12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'amp_20q13.31' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.4e-06 (Fisher's exact test), Q value = 0.0023

Table S24.  Gene #27: 'amp_20q13.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 438 162
AMP PEAK 27(20Q13.31) MUTATED 315 145
AMP PEAK 27(20Q13.31) WILD-TYPE 123 17

Figure S24.  Get High-res Image Gene #27: 'amp_20q13.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'amp_20q13.31' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S25.  Gene #27: 'amp_20q13.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
AMP PEAK 27(20Q13.31) MUTATED 289 25 136 7
AMP PEAK 27(20Q13.31) WILD-TYPE 89 34 10 6

Figure S25.  Get High-res Image Gene #27: 'amp_20q13.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_1p36.11' versus 'PATHOLOGY.M.STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.11

Table S26.  Gene #28: 'del_1p36.11' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 446 74 10 2 63
DEL PEAK 1(1P36.11) MUTATED 160 46 6 0 24
DEL PEAK 1(1P36.11) WILD-TYPE 286 28 4 2 39

Figure S26.  Get High-res Image Gene #28: 'del_1p36.11' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

'del_4p16.2' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.05e-05 (Fisher's exact test), Q value = 0.028

Table S27.  Gene #36: 'del_4p16.2' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients NO YES
ALL 9 595
DEL PEAK 9(4P16.2) MUTATED 9 184
DEL PEAK 9(4P16.2) WILD-TYPE 0 411

Figure S27.  Get High-res Image Gene #36: 'del_4p16.2' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'del_4p16.2' versus 'NUMBER.OF.LYMPH.NODES'

P value = 9.72e-05 (Wilcoxon-test), Q value = 0.087

Table S28.  Gene #36: 'del_4p16.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 9(4P16.2) MUTATED 185 3.2 (5.5)
DEL PEAK 9(4P16.2) WILD-TYPE 385 1.7 (4.2)

Figure S28.  Get High-res Image Gene #36: 'del_4p16.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_4q22.1' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000108 (Wilcoxon-test), Q value = 0.096

Table S29.  Gene #37: 'del_4q22.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 10(4Q22.1) MUTATED 204 3.1 (5.5)
DEL PEAK 10(4Q22.1) WILD-TYPE 366 1.7 (4.1)

Figure S29.  Get High-res Image Gene #37: 'del_4q22.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_4q35.1' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000206 (Wilcoxon-test), Q value = 0.18

Table S30.  Gene #38: 'del_4q35.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 11(4Q35.1) MUTATED 213 2.9 (4.9)
DEL PEAK 11(4Q35.1) WILD-TYPE 357 1.8 (4.5)

Figure S30.  Get High-res Image Gene #38: 'del_4q35.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_5q12.1' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000104 (Fisher's exact test), Q value = 0.093

Table S31.  Gene #39: 'del_5q12.1' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients NO YES
ALL 9 595
DEL PEAK 12(5Q12.1) MUTATED 8 145
DEL PEAK 12(5Q12.1) WILD-TYPE 1 450

Figure S31.  Get High-res Image Gene #39: 'del_5q12.1' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'del_8p23.2' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.01e-05 (Fisher's exact test), Q value = 0.063

Table S32.  Gene #45: 'del_8p23.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 438 162
DEL PEAK 18(8P23.2) MUTATED 184 98
DEL PEAK 18(8P23.2) WILD-TYPE 254 64

Figure S32.  Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'del_8p23.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.045

Table S33.  Gene #45: 'del_8p23.2' versus Clinical Feature #4: '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 102 1 36 171 10 3 26 21 78 53 61 27 2
DEL PEAK 18(8P23.2) MUTATED 39 0 12 64 3 2 14 11 42 33 44 14 1
DEL PEAK 18(8P23.2) WILD-TYPE 63 1 24 107 7 1 12 10 36 20 17 13 1

Figure S33.  Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'del_8p23.2' versus 'PATHOLOGY.N.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S34.  Gene #45: 'del_8p23.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
DEL PEAK 18(8P23.2) MUTATED 131 79 72
DEL PEAK 18(8P23.2) WILD-TYPE 210 69 40

Figure S34.  Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_8p23.2' versus 'HISTOLOGICAL.TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.063

Table S35.  Gene #45: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
DEL PEAK 18(8P23.2) MUTATED 167 16 89 7
DEL PEAK 18(8P23.2) WILD-TYPE 211 43 57 6

Figure S35.  Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_8p23.2' versus 'NUMBER.OF.LYMPH.NODES'

P value = 3.56e-06 (Wilcoxon-test), Q value = 0.0033

Table S36.  Gene #45: 'del_8p23.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 18(8P23.2) MUTATED 272 3.0 (5.8)
DEL PEAK 18(8P23.2) WILD-TYPE 298 1.5 (3.3)

Figure S36.  Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_8p22' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S37.  Gene #46: 'del_8p22' versus Clinical Feature #4: '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 102 1 36 171 10 3 26 21 78 53 61 27 2
DEL PEAK 19(8P22) MUTATED 38 0 13 66 3 2 14 13 44 36 44 17 1
DEL PEAK 19(8P22) WILD-TYPE 64 1 23 105 7 1 12 8 34 17 17 10 1

Figure S37.  Get High-res Image Gene #46: 'del_8p22' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'del_8p22' versus 'PATHOLOGY.N.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S38.  Gene #46: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
DEL PEAK 19(8P22) MUTATED 134 82 78
DEL PEAK 19(8P22) WILD-TYPE 207 66 34

Figure S38.  Get High-res Image Gene #46: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_8p22' versus 'HISTOLOGICAL.TYPE'

P value = 1e-04 (Fisher's exact test), Q value = 0.089

Table S39.  Gene #46: 'del_8p22' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
DEL PEAK 19(8P22) MUTATED 178 17 89 7
DEL PEAK 19(8P22) WILD-TYPE 200 42 57 6

Figure S39.  Get High-res Image Gene #46: 'del_8p22' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_8p22' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.28e-08 (Wilcoxon-test), Q value = 4.1e-05

Table S40.  Gene #46: 'del_8p22' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 19(8P22) MUTATED 285 3.1 (5.7)
DEL PEAK 19(8P22) WILD-TYPE 285 1.4 (3.3)

Figure S40.  Get High-res Image Gene #46: 'del_8p22' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_14q11.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S41.  Gene #56: 'del_14q11.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
DEL PEAK 29(14Q11.2) MUTATED 129 5 66 2
DEL PEAK 29(14Q11.2) WILD-TYPE 249 54 80 11

Figure S41.  Get High-res Image Gene #56: 'del_14q11.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_14q31.1' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S42.  Gene #57: 'del_14q31.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
DEL PEAK 30(14Q31.1) MUTATED 136 5 65 1
DEL PEAK 30(14Q31.1) WILD-TYPE 242 54 81 12

Figure S42.  Get High-res Image Gene #57: 'del_14q31.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_17p12' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00023 (Fisher's exact test), Q value = 0.2

Table S43.  Gene #64: 'del_17p12' versus Clinical Feature #4: '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 102 1 36 171 10 3 26 21 78 53 61 27 2
DEL PEAK 37(17P12) MUTATED 52 0 19 87 3 1 16 16 51 41 45 20 2
DEL PEAK 37(17P12) WILD-TYPE 50 1 17 84 7 2 10 5 27 12 16 7 0

Figure S43.  Get High-res Image Gene #64: 'del_17p12' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'del_17p12' versus 'PATHOLOGY.N.STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.054

Table S44.  Gene #64: 'del_17p12' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
DEL PEAK 37(17P12) MUTATED 177 101 81
DEL PEAK 37(17P12) WILD-TYPE 164 47 31

Figure S44.  Get High-res Image Gene #64: 'del_17p12' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_17p12' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S45.  Gene #64: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
DEL PEAK 37(17P12) MUTATED 227 16 105 6
DEL PEAK 37(17P12) WILD-TYPE 151 43 41 7

Figure S45.  Get High-res Image Gene #64: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_17p12' versus 'NUMBER.OF.LYMPH.NODES'

P value = 9.69e-06 (Wilcoxon-test), Q value = 0.0091

Table S46.  Gene #64: 'del_17p12' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 37(17P12) MUTATED 341 2.7 (5.2)
DEL PEAK 37(17P12) WILD-TYPE 229 1.5 (3.8)

Figure S46.  Get High-res Image Gene #64: 'del_17p12' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_17q24.3' versus 'NUMBER.OF.LYMPH.NODES'

P value = 5.44e-05 (Wilcoxon-test), Q value = 0.049

Table S47.  Gene #65: 'del_17q24.3' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 38(17Q24.3) MUTATED 89 3.2 (4.5)
DEL PEAK 38(17Q24.3) WILD-TYPE 481 2.0 (4.7)

Figure S47.  Get High-res Image Gene #65: 'del_17q24.3' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_18p11.31' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.45e-06 (Fisher's exact test), Q value = 0.0023

Table S48.  Gene #66: 'del_18p11.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 438 162
DEL PEAK 39(18P11.31) MUTATED 238 122
DEL PEAK 39(18P11.31) WILD-TYPE 200 40

Figure S48.  Get High-res Image Gene #66: 'del_18p11.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'del_18p11.31' versus 'NEOPLASM.DISEASESTAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.08

Table S49.  Gene #66: 'del_18p11.31' versus Clinical Feature #4: '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 102 1 36 171 10 3 26 21 78 53 61 27 2
DEL PEAK 39(18P11.31) MUTATED 56 0 14 96 4 3 12 13 51 34 47 24 1
DEL PEAK 39(18P11.31) WILD-TYPE 46 1 22 75 6 0 14 8 27 19 14 3 1

Figure S49.  Get High-res Image Gene #66: 'del_18p11.31' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'del_18p11.31' versus 'PATHOLOGY.M.STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.027

Table S50.  Gene #66: 'del_18p11.31' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 446 74 10 2 63
DEL PEAK 39(18P11.31) MUTATED 253 60 10 1 35
DEL PEAK 39(18P11.31) WILD-TYPE 193 14 0 1 28

Figure S50.  Get High-res Image Gene #66: 'del_18p11.31' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

'del_18p11.31' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S51.  Gene #66: 'del_18p11.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
DEL PEAK 39(18P11.31) MUTATED 227 10 116 6
DEL PEAK 39(18P11.31) WILD-TYPE 151 49 30 7

Figure S51.  Get High-res Image Gene #66: 'del_18p11.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_18q12.2' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.4e-09 (Fisher's exact test), Q value = 1.3e-06

Table S52.  Gene #67: 'del_18q12.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 438 162
DEL PEAK 40(18Q12.2) MUTATED 266 139
DEL PEAK 40(18Q12.2) WILD-TYPE 172 23

Figure S52.  Get High-res Image Gene #67: 'del_18q12.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'del_18q12.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00026 (Fisher's exact test), Q value = 0.23

Table S53.  Gene #67: 'del_18q12.2' versus Clinical Feature #4: '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 102 1 36 171 10 3 26 21 78 53 61 27 2
DEL PEAK 40(18Q12.2) MUTATED 59 0 21 105 4 3 15 17 58 40 52 23 1
DEL PEAK 40(18Q12.2) WILD-TYPE 43 1 15 66 6 0 11 4 20 13 9 4 1

Figure S53.  Get High-res Image Gene #67: 'del_18q12.2' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'del_18q12.2' versus 'PATHOLOGY.N.STAGE'

P value = 7e-05 (Fisher's exact test), Q value = 0.063

Table S54.  Gene #67: 'del_18q12.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
DEL PEAK 40(18Q12.2) MUTATED 205 114 86
DEL PEAK 40(18Q12.2) WILD-TYPE 136 34 26

Figure S54.  Get High-res Image Gene #67: 'del_18q12.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_18q12.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S55.  Gene #67: 'del_18q12.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
DEL PEAK 40(18Q12.2) MUTATED 250 15 128 10
DEL PEAK 40(18Q12.2) WILD-TYPE 128 44 18 3

Figure S55.  Get High-res Image Gene #67: 'del_18q12.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_18q12.2' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000195 (Wilcoxon-test), Q value = 0.17

Table S56.  Gene #67: 'del_18q12.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 40(18Q12.2) MUTATED 386 2.5 (5.0)
DEL PEAK 40(18Q12.2) WILD-TYPE 184 1.6 (3.9)

Figure S56.  Get High-res Image Gene #67: 'del_18q12.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_18q21.2' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.46e-09 (Fisher's exact test), Q value = 3.3e-06

Table S57.  Gene #68: 'del_18q21.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 438 162
DEL PEAK 41(18Q21.2) MUTATED 280 142
DEL PEAK 41(18Q21.2) WILD-TYPE 158 20

Figure S57.  Get High-res Image Gene #68: 'del_18q21.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'del_18q21.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S58.  Gene #68: 'del_18q21.2' versus Clinical Feature #4: '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 102 1 36 171 10 3 26 21 78 53 61 27 2
DEL PEAK 41(18Q21.2) MUTATED 61 0 23 107 4 3 16 17 61 43 55 24 2
DEL PEAK 41(18Q21.2) WILD-TYPE 41 1 13 64 6 0 10 4 17 10 6 3 0

Figure S58.  Get High-res Image Gene #68: 'del_18q21.2' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'del_18q21.2' versus 'PATHOLOGY.N.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S59.  Gene #68: 'del_18q21.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
DEL PEAK 41(18Q21.2) MUTATED 211 118 93
DEL PEAK 41(18Q21.2) WILD-TYPE 130 30 19

Figure S59.  Get High-res Image Gene #68: 'del_18q21.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_18q21.2' versus 'PATHOLOGY.M.STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.12

Table S60.  Gene #68: 'del_18q21.2' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 446 74 10 2 63
DEL PEAK 41(18Q21.2) MUTATED 301 67 9 2 42
DEL PEAK 41(18Q21.2) WILD-TYPE 145 7 1 0 21

Figure S60.  Get High-res Image Gene #68: 'del_18q21.2' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

'del_18q21.2' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S61.  Gene #68: 'del_18q21.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
DEL PEAK 41(18Q21.2) MUTATED 262 17 129 11
DEL PEAK 41(18Q21.2) WILD-TYPE 116 42 17 2

Figure S61.  Get High-res Image Gene #68: 'del_18q21.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_18q21.2' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.61e-06 (Wilcoxon-test), Q value = 0.0015

Table S62.  Gene #68: 'del_18q21.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 41(18Q21.2) MUTATED 402 2.6 (5.0)
DEL PEAK 41(18Q21.2) WILD-TYPE 168 1.4 (3.9)

Figure S62.  Get High-res Image Gene #68: 'del_18q21.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_18q22.1' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.6e-07 (Fisher's exact test), Q value = 0.00015

Table S63.  Gene #69: 'del_18q22.1' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 438 162
DEL PEAK 42(18Q22.1) MUTATED 279 138
DEL PEAK 42(18Q22.1) WILD-TYPE 159 24

Figure S63.  Get High-res Image Gene #69: 'del_18q22.1' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'del_18q22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S64.  Gene #69: 'del_18q22.1' versus Clinical Feature #4: '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 102 1 36 171 10 3 26 21 78 53 61 27 2
DEL PEAK 42(18Q22.1) MUTATED 61 0 23 107 4 3 14 16 60 43 54 24 2
DEL PEAK 42(18Q22.1) WILD-TYPE 41 1 13 64 6 0 12 5 18 10 7 3 0

Figure S64.  Get High-res Image Gene #69: 'del_18q22.1' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'del_18q22.1' versus 'PATHOLOGY.N.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S65.  Gene #69: 'del_18q22.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
DEL PEAK 42(18Q22.1) MUTATED 211 114 92
DEL PEAK 42(18Q22.1) WILD-TYPE 130 34 20

Figure S65.  Get High-res Image Gene #69: 'del_18q22.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_18q22.1' versus 'PATHOLOGY.M.STAGE'

P value = 0.00027 (Fisher's exact test), Q value = 0.24

Table S66.  Gene #69: 'del_18q22.1' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 446 74 10 2 63
DEL PEAK 42(18Q22.1) MUTATED 298 66 9 2 41
DEL PEAK 42(18Q22.1) WILD-TYPE 148 8 1 0 22

Figure S66.  Get High-res Image Gene #69: 'del_18q22.1' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

'del_18q22.1' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0094

Table S67.  Gene #69: 'del_18q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
DEL PEAK 42(18Q22.1) MUTATED 262 16 127 10
DEL PEAK 42(18Q22.1) WILD-TYPE 116 43 19 3

Figure S67.  Get High-res Image Gene #69: 'del_18q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_18q22.1' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.54e-05 (Wilcoxon-test), Q value = 0.014

Table S68.  Gene #69: 'del_18q22.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 42(18Q22.1) MUTATED 399 2.6 (5.0)
DEL PEAK 42(18Q22.1) WILD-TYPE 171 1.4 (3.8)

Figure S68.  Get High-res Image Gene #69: 'del_18q22.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_19p13.3' versus 'PATHOLOGY.N.STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.089

Table S69.  Gene #70: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
DEL PEAK 43(19P13.3) MUTATED 37 27 31
DEL PEAK 43(19P13.3) WILD-TYPE 304 121 81

Figure S69.  Get High-res Image Gene #70: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_19p13.3' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.71e-06 (Wilcoxon-test), Q value = 0.0044

Table S70.  Gene #70: 'del_19p13.3' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 43(19P13.3) MUTATED 90 3.9 (6.0)
DEL PEAK 43(19P13.3) WILD-TYPE 480 1.9 (4.4)

Figure S70.  Get High-res Image Gene #70: 'del_19p13.3' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_21q11.2' versus 'HISTOLOGICAL.TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.072

Table S71.  Gene #72: 'del_21q11.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 378 59 146 13
DEL PEAK 45(21Q11.2) MUTATED 126 8 66 3
DEL PEAK 45(21Q11.2) WILD-TYPE 252 51 80 10

Figure S71.  Get High-res Image Gene #72: 'del_21q11.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_22q13.32' versus 'PATHOLOGY.N.STAGE'

P value = 0.00028 (Fisher's exact test), Q value = 0.25

Table S72.  Gene #73: 'del_22q13.32' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 341 148 112
DEL PEAK 46(22Q13.32) MUTATED 102 70 49
DEL PEAK 46(22Q13.32) WILD-TYPE 239 78 63

Figure S72.  Get High-res Image Gene #73: 'del_22q13.32' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_22q13.32' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000266 (Wilcoxon-test), Q value = 0.23

Table S73.  Gene #73: 'del_22q13.32' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 570 2.2 (4.7)
DEL PEAK 46(22Q13.32) MUTATED 210 2.9 (5.2)
DEL PEAK 46(22Q13.32) WILD-TYPE 360 1.8 (4.4)

Figure S73.  Get High-res Image Gene #73: 'del_22q13.32' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = COADREAD-TP.merged_data.txt

  • Number of patients = 604

  • Number of significantly focal cnvs = 73

  • Number of selected clinical features = 13

  • 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

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

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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] 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)
[3] 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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