Correlation between copy number variation genes (focal events) and selected clinical features
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 focal events and 13 clinical features across 592 patients, 63 significant findings detected with Q value < 0.25.

  • amp_6p21.1 cnv correlated to 'PATHOLOGY.N.STAGE'.

  • 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_20p11.23 cnv correlated to 'PATHOLOGY.M.STAGE'.

  • 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',  'NEOPLASM.DISEASESTAGE', and 'HISTOLOGICAL.TYPE'.

  • del_1p36.11 cnv correlated to 'PATHOLOGY.M.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • del_4p16.1 cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION' and 'NUMBER.OF.LYMPH.NODES'.

  • del_5q11.2 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_14q31.1 cnv correlated to 'HISTOLOGICAL.TYPE'.

  • del_17p12 cnv correlated to 'PATHOLOGY.N.STAGE',  'HISTOLOGICAL.TYPE', and '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',  'PATHOLOGY.N.STAGE', and 'HISTOLOGICAL.TYPE'.

  • 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',  'HISTOLOGICAL.TYPE', and 'NUMBER.OF.LYMPH.NODES'.

  • del_19p13.3 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 75 focal events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 63 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 2 414 (70%) 178 0.744
(1.00) 		0.0269
(1.00) 		1.3e-09
(1.27e-06) 		1e-05
(0.00965) 		0.353
(1.00) 		1e-05
(0.00965) 		0.00019
(0.175) 		0.0882
(1.00) 		1e-05
(0.00965) 		0.0636
(1.00) 		0.0492
(1.00) 		2.2e-06
(0.00214) 		0.335
(1.00)
del 8p23 2 278 (47%) 314 0.625
(1.00) 		0.13
(1.00) 		3.96e-05
(0.0371) 		0.00017
(0.157) 		0.0775
(1.00) 		5e-05
(0.0467) 		0.00332
(1.00) 		0.07
(1.00) 		3e-05
(0.0282) 		0.0908
(1.00) 		0.00843
(1.00) 		1.86e-05
(0.0176) 		0.571
(1.00)
del 18q22 1 409 (69%) 183 0.84
(1.00) 		0.0998
(1.00) 		2.25e-07
(0.000219) 		2e-05
(0.0189) 		0.514
(1.00) 		2e-05
(0.0189) 		0.00033
(0.3) 		0.154
(1.00) 		1e-05
(0.00965) 		0.0632
(1.00) 		0.0934
(1.00) 		2.73e-05
(0.0257) 		0.219
(1.00)
amp 13q12 13 384 (65%) 208 0.187
(1.00) 		0.392
(1.00) 		0.000923
(0.818) 		5e-05
(0.0467) 		0.775
(1.00) 		4e-05
(0.0374) 		0.00219
(1.00) 		0.667
(1.00) 		1e-05
(0.00965) 		0.505
(1.00) 		0.0502
(1.00) 		0.000111
(0.102) 		0.0157
(1.00)
amp 13q12 2 379 (64%) 213 0.27
(1.00) 		0.341
(1.00) 		0.000699
(0.622) 		0.00025
(0.229) 		0.797
(1.00) 		5e-05
(0.0467) 		0.00783
(1.00) 		0.493
(1.00) 		1e-05
(0.00965) 		0.5
(1.00) 		0.0895
(1.00) 		0.000139
(0.128) 		0.0209
(1.00)
del 8p22 292 (49%) 300 0.211
(1.00) 		0.164
(1.00) 		0.000291
(0.265) 		2e-05
(0.0189) 		0.0641
(1.00) 		1e-05
(0.00965) 		0.00095
(0.841) 		0.162
(1.00) 		0.00013
(0.12) 		0.0191
(1.00) 		0.0113
(1.00) 		3.88e-07
(0.000377) 		0.561
(1.00)
del 18p11 31 352 (59%) 240 0.611
(1.00) 		0.0178
(1.00) 		3.13e-06
(0.00304) 		0.00024
(0.22) 		0.934
(1.00) 		0.011
(1.00) 		3e-05
(0.0282) 		0.802
(1.00) 		1e-05
(0.00965) 		0.324
(1.00) 		0.0187
(1.00) 		0.0142
(1.00) 		0.729
(1.00)
amp 20q12 452 (76%) 140 0.664
(1.00) 		0.432
(1.00) 		3.44e-06
(0.00333) 		6e-05
(0.0559) 		0.379
(1.00) 		0.00088
(0.781) 		0.00061
(0.545) 		0.289
(1.00) 		1e-05
(0.00965) 		0.693
(1.00) 		0.0515
(1.00) 		0.00678
(1.00) 		0.151
(1.00)
amp 20q13 31 455 (77%) 137 0.614
(1.00) 		0.46
(1.00) 		5.34e-06
(0.00516) 		0.00016
(0.148) 		0.237
(1.00) 		0.00112
(0.988) 		0.00097
(0.857) 		0.494
(1.00) 		1e-05
(0.00965) 		0.692
(1.00) 		0.0534
(1.00) 		0.0062
(1.00) 		0.153
(1.00)
del 17p12 353 (60%) 239 0.606
(1.00) 		0.146
(1.00) 		0.00179
(1.00) 		0.00031
(0.282) 		0.477
(1.00) 		9e-05
(0.0835) 		0.0179
(1.00) 		0.503
(1.00) 		1e-05
(0.00965) 		0.325
(1.00) 		0.157
(1.00) 		1.86e-05
(0.0176) 		0.478
(1.00)
del 18q12 2 396 (67%) 196 0.706
(1.00) 		0.0256
(1.00) 		1.14e-09
(1.11e-06) 		0.00029
(0.264) 		0.375
(1.00) 		0.00015
(0.139) 		0.00087
(0.773) 		0.382
(1.00) 		1e-05
(0.00965) 		0.0335
(1.00) 		0.0513
(1.00) 		0.000515
(0.463) 		0.145
(1.00)
amp 13q22 1 382 (65%) 210 0.292
(1.00) 		0.606
(1.00) 		0.0257
(1.00) 		0.00169
(1.00) 		0.694
(1.00) 		3e-05
(0.0282) 		0.0138
(1.00) 		0.197
(1.00) 		1e-05
(0.00965) 		0.503
(1.00) 		0.271
(1.00) 		0.000615
(0.549) 		0.0814
(1.00)
amp 16p11 2 165 (28%) 427 0.909
(1.00) 		0.34
(1.00) 		0.918
(1.00) 		0.00059
(0.528) 		0.722
(1.00) 		5e-05
(0.0467) 		0.16
(1.00) 		0.927
(1.00) 		0.00202
(1.00) 		0.273
(1.00) 		0.245
(1.00) 		6.58e-05
(0.0612) 		0.556
(1.00)
amp 20q11 21 450 (76%) 142 0.538
(1.00) 		0.524
(1.00) 		6.64e-06
(0.00641) 		0.00032
(0.291) 		0.285
(1.00) 		0.00146
(1.00) 		0.00411
(1.00) 		0.29
(1.00) 		1e-05
(0.00965) 		0.694
(1.00) 		0.0504
(1.00) 		0.00652
(1.00) 		0.249
(1.00)
del 1p36 11 234 (40%) 358 0.101
(1.00) 		0.0457
(1.00) 		0.155
(1.00) 		0.00631
(1.00) 		0.371
(1.00) 		0.00279
(1.00) 		0.0002
(0.184) 		0.238
(1.00) 		0.00344
(1.00) 		0.745
(1.00) 		0.084
(1.00) 		0.000259
(0.237) 		0.302
(1.00)
del 4p16 1 190 (32%) 402 0.263
(1.00) 		0.708
(1.00) 		0.0468
(1.00) 		0.00891
(1.00) 		0.988
(1.00) 		0.0011
(0.971) 		0.00962
(1.00) 		0.134
(1.00) 		0.0175
(1.00) 		3.17e-05
(0.0297) 		0.0698
(1.00) 		0.000257
(0.235) 		0.401
(1.00)
del 19p13 3 93 (16%) 499 0.51
(1.00) 		0.317
(1.00) 		0.0415
(1.00) 		0.00208
(1.00) 		0.382
(1.00) 		0.00018
(0.166) 		0.0167
(1.00) 		0.497
(1.00) 		0.0532
(1.00) 		0.638
(1.00) 		0.143
(1.00) 		3.4e-06
(0.00329) 		0.814
(1.00)
amp 6p21 1 148 (25%) 444 0.628
(1.00) 		0.682
(1.00) 		0.0237
(1.00) 		0.0365
(1.00) 		0.199
(1.00) 		0.00021
(0.193) 		0.111
(1.00) 		0.128
(1.00) 		0.00157
(1.00) 		0.00123
(1.00) 		0.0875
(1.00) 		0.00052
(0.467) 		0.131
(1.00)
amp 20p11 23 311 (53%) 281 0.706
(1.00) 		0.969
(1.00) 		0.0255
(1.00) 		0.00034
(0.308) 		0.919
(1.00) 		0.0457
(1.00) 		0.00027
(0.247) 		0.0585
(1.00) 		0.00045
(0.405) 		0.181
(1.00) 		0.249
(1.00) 		0.0653
(1.00) 		0.741
(1.00)
amp 20p11 21 349 (59%) 243 0.607
(1.00) 		0.654
(1.00) 		0.00818
(1.00) 		0.00398
(1.00) 		0.82
(1.00) 		0.425
(1.00) 		0.00061
(0.545) 		0.0655
(1.00) 		1e-05
(0.00965) 		0.32
(1.00) 		0.502
(1.00) 		0.594
(1.00) 		0.615
(1.00)
del 5q11 2 147 (25%) 445 0.214
(1.00) 		0.164
(1.00) 		0.0184
(1.00) 		0.0305
(1.00) 		1
(1.00) 		0.00711
(1.00) 		0.0231
(1.00) 		0.775
(1.00) 		0.00594
(1.00) 		8.86e-05
(0.0823) 		0.711
(1.00) 		0.00444
(1.00) 		0.394
(1.00)
del 14q11 2 200 (34%) 392 0.491
(1.00) 		0.29
(1.00) 		0.014
(1.00) 		0.792
(1.00) 		0.315
(1.00) 		0.0274
(1.00) 		0.301
(1.00) 		1
(1.00) 		1e-05
(0.00965) 		0.495
(1.00) 		0.882
(1.00) 		0.241
(1.00) 		0.919
(1.00)
del 14q31 1 207 (35%) 385 0.87
(1.00) 		0.172
(1.00) 		0.0255
(1.00) 		0.363
(1.00) 		0.212
(1.00) 		0.0366
(1.00) 		0.0382
(1.00) 		0.342
(1.00) 		2e-05
(0.0189) 		0.506
(1.00) 		0.737
(1.00) 		0.0938
(1.00) 		0.978
(1.00)
del 14q31 1 208 (35%) 384 0.764
(1.00) 		0.186
(1.00) 		0.0516
(1.00) 		0.422
(1.00) 		0.198
(1.00) 		0.0141
(1.00) 		0.0416
(1.00) 		0.301
(1.00) 		2e-05
(0.0189) 		0.505
(1.00) 		0.736
(1.00) 		0.06
(1.00) 		0.978
(1.00)
amp 1q31 1 141 (24%) 451 0.574
(1.00) 		0.24
(1.00) 		0.0489
(1.00) 		0.282
(1.00) 		0.235
(1.00) 		0.0521
(1.00) 		0.123
(1.00) 		0.209
(1.00) 		0.109
(1.00) 		0.0391
(1.00) 		0.739
(1.00) 		0.00807
(1.00) 		1
(1.00)
amp 2q33 1 131 (22%) 461 0.0437
(1.00) 		0.6
(1.00) 		0.0138
(1.00) 		0.0468
(1.00) 		0.927
(1.00) 		0.00436
(1.00) 		0.278
(1.00) 		0.921
(1.00) 		0.00119
(1.00) 		0.115
(1.00) 		0.392
(1.00) 		0.00595
(1.00) 		0.398
(1.00)
amp 5p12 110 (19%) 482 0.0488
(1.00) 		0.249
(1.00) 		0.0568
(1.00) 		0.366
(1.00) 		0.394
(1.00) 		0.119
(1.00) 		0.322
(1.00) 		0.832
(1.00) 		0.0199
(1.00) 		0.379
(1.00) 		0.0283
(1.00) 		0.0363
(1.00) 		0.816
(1.00)
amp 5q22 3 63 (11%) 529 0.282
(1.00) 		0.969
(1.00) 		0.371
(1.00) 		0.545
(1.00) 		0.961
(1.00) 		0.29
(1.00) 		0.0596
(1.00) 		0.895
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.0728
(1.00) 		0.163
(1.00) 		0.459
(1.00)
amp 8p11 23 203 (34%) 389 0.298
(1.00) 		0.836
(1.00) 		0.626
(1.00) 		0.272
(1.00) 		0.466
(1.00) 		0.565
(1.00) 		0.373
(1.00) 		0.544
(1.00) 		0.194
(1.00) 		0.501
(1.00) 		0.173
(1.00) 		0.928
(1.00) 		0.631
(1.00)
amp 8p11 21 246 (42%) 346 0.665
(1.00) 		0.545
(1.00) 		0.639
(1.00) 		0.0969
(1.00) 		0.518
(1.00) 		0.392
(1.00) 		0.242
(1.00) 		0.182
(1.00) 		0.1
(1.00) 		0.742
(1.00) 		0.0429
(1.00) 		0.57
(1.00) 		0.427
(1.00)
amp 8q12 1 318 (54%) 274 0.681
(1.00) 		0.13
(1.00) 		0.305
(1.00) 		0.0707
(1.00) 		0.334
(1.00) 		0.135
(1.00) 		0.0263
(1.00) 		0.458
(1.00) 		0.00714
(1.00) 		0.0423
(1.00) 		0.101
(1.00) 		0.14
(1.00) 		0.437
(1.00)
amp 8q24 21 353 (60%) 239 0.311
(1.00) 		0.186
(1.00) 		0.0719
(1.00) 		0.154
(1.00) 		0.299
(1.00) 		0.24
(1.00) 		0.0665
(1.00) 		0.315
(1.00) 		0.00735
(1.00) 		0.0917
(1.00) 		0.209
(1.00) 		0.273
(1.00) 		0.541
(1.00)
amp 10q22 3 36 (6%) 556 0.722
(1.00) 		0.428
(1.00) 		1
(1.00) 		0.45
(1.00) 		0.267
(1.00) 		0.0142
(1.00) 		0.604
(1.00) 		0.606
(1.00) 		0.952
(1.00) 		0.434
(1.00) 		0.922
(1.00) 		0.0244
(1.00) 		0.541
(1.00)
amp 11p15 5 132 (22%) 460 0.571
(1.00) 		0.0543
(1.00) 		0.0931
(1.00) 		0.91
(1.00) 		0.372
(1.00) 		0.62
(1.00) 		0.273
(1.00) 		0.693
(1.00) 		0.00086
(0.765) 		0.117
(1.00) 		0.89
(1.00) 		0.547
(1.00) 		0.526
(1.00)
amp 12p13 32 146 (25%) 446 0.293
(1.00) 		0.104
(1.00) 		0.914
(1.00) 		0.11
(1.00) 		0.389
(1.00) 		0.118
(1.00) 		0.148
(1.00) 		0.849
(1.00) 		0.464
(1.00) 		0.696
(1.00) 		0.783
(1.00) 		0.399
(1.00) 		0.655
(1.00)
amp 15q26 1 42 (7%) 550 0.3
(1.00) 		0.704
(1.00) 		0.589
(1.00) 		0.115
(1.00) 		0.292
(1.00) 		0.00165
(1.00) 		0.54
(1.00) 		0.199
(1.00) 		0.521
(1.00) 		0.129
(1.00) 		0.493
(1.00) 		0.00318
(1.00) 		1
(1.00)
amp 17q12 150 (25%) 442 0.126
(1.00) 		0.454
(1.00) 		0.596
(1.00) 		0.189
(1.00) 		0.332
(1.00) 		0.207
(1.00) 		0.00522
(1.00) 		0.0887
(1.00) 		0.431
(1.00) 		0.461
(1.00) 		0.0303
(1.00) 		0.251
(1.00) 		0.346
(1.00)
amp 17q24 1 135 (23%) 457 0.0194
(1.00) 		0.438
(1.00) 		1
(1.00) 		0.551
(1.00) 		0.924
(1.00) 		0.885
(1.00) 		0.0363
(1.00) 		0.624
(1.00) 		0.0686
(1.00) 		0.692
(1.00) 		0.121
(1.00) 		0.835
(1.00) 		0.941
(1.00)
amp 19p13 2 104 (18%) 488 0.376
(1.00) 		0.884
(1.00) 		0.18
(1.00) 		0.639
(1.00) 		0.441
(1.00) 		0.0443
(1.00) 		0.301
(1.00) 		0.16
(1.00) 		0.0443
(1.00) 		1
(1.00) 		0.121
(1.00) 		0.457
(1.00) 		0.928
(1.00)
amp 19q12 131 (22%) 461 0.946
(1.00) 		0.768
(1.00) 		0.148
(1.00) 		0.385
(1.00) 		0.784
(1.00) 		0.0667
(1.00) 		0.0447
(1.00) 		0.165
(1.00) 		0.0185
(1.00) 		1
(1.00) 		0.389
(1.00) 		0.261
(1.00) 		0.915
(1.00)
amp xq28 120 (20%) 472 0.0862
(1.00) 		0.38
(1.00) 		0.488
(1.00) 		0.09
(1.00) 		0.501
(1.00) 		0.0408
(1.00) 		0.251
(1.00) 		0.683
(1.00) 		0.0343
(1.00) 		0.695
(1.00) 		0.299
(1.00) 		0.0629
(1.00) 		0.575
(1.00)
del 1p33 167 (28%) 425 0.0375
(1.00) 		0.689
(1.00) 		0.535
(1.00) 		0.047
(1.00) 		0.35
(1.00) 		0.0169
(1.00) 		0.0127
(1.00) 		0.715
(1.00) 		0.0493
(1.00) 		0.717
(1.00) 		0.275
(1.00) 		0.00471
(1.00) 		0.407
(1.00)
del 1p13 2 167 (28%) 425 0.0576
(1.00) 		0.776
(1.00) 		0.301
(1.00) 		0.0102
(1.00) 		0.208
(1.00) 		0.0058
(1.00) 		0.00226
(1.00) 		0.584
(1.00) 		0.0976
(1.00) 		0.279
(1.00) 		0.371
(1.00) 		0.000545
(0.489) 		0.444
(1.00)
del 2p12 21 (4%) 571 0.968
(1.00) 		0.146
(1.00) 		0.000676
(0.603) 		0.399
(1.00) 		1
(1.00) 		0.397
(1.00) 		0.351
(1.00) 		0.66
(1.00) 		0.00707
(1.00) 		0.279
(1.00) 		0.887
(1.00) 		0.382
(1.00) 		1
(1.00)
del 2q22 1 34 (6%) 558 1
(1.00) 		0.721
(1.00) 		0.696
(1.00) 		0.399
(1.00) 		0.635
(1.00) 		0.715
(1.00) 		0.405
(1.00) 		0.596
(1.00) 		0.982
(1.00) 		1
(1.00) 		1
(1.00) 		0.35
(1.00) 		0.0107
(1.00)
del 2q37 2 31 (5%) 561 0.837
(1.00) 		0.0887
(1.00) 		0.534
(1.00) 		0.217
(1.00) 		0.428
(1.00) 		0.147
(1.00) 		0.0773
(1.00) 		0.363
(1.00) 		0.866
(1.00) 		1
(1.00) 		0.385
(1.00) 		0.124
(1.00) 		0.0801
(1.00)
del 3p26 3 89 (15%) 503 0.0542
(1.00) 		0.428
(1.00) 		0.433
(1.00) 		0.0282
(1.00) 		0.08
(1.00) 		0.011
(1.00) 		0.00273
(1.00) 		0.731
(1.00) 		0.0916
(1.00) 		0.631
(1.00) 		0.0617
(1.00) 		0.00666
(1.00) 		0.677
(1.00)
del 3p14 2 110 (19%) 482 0.126
(1.00) 		0.339
(1.00) 		0.633
(1.00) 		0.14
(1.00) 		0.106
(1.00) 		0.164
(1.00) 		0.0473
(1.00) 		0.525
(1.00) 		0.484
(1.00) 		0.676
(1.00) 		0.241
(1.00) 		0.0673
(1.00) 		0.856
(1.00)
del 3q26 31 60 (10%) 532 0.887
(1.00) 		0.81
(1.00) 		0.878
(1.00) 		0.00514
(1.00) 		0.0189
(1.00) 		0.75
(1.00) 		0.39
(1.00) 		0.103
(1.00) 		0.0243
(1.00) 		1
(1.00) 		0.425
(1.00) 		0.576
(1.00) 		0.0581
(1.00)
del 4q22 1 210 (35%) 382 0.407
(1.00) 		0.177
(1.00) 		0.0114
(1.00) 		0.0253
(1.00) 		0.157
(1.00) 		0.00119
(1.00) 		0.431
(1.00) 		0.169
(1.00) 		0.00143
(1.00) 		0.00143
(1.00) 		0.752
(1.00) 		0.000396
(0.357) 		0.813
(1.00)
del 4q35 1 219 (37%) 373 0.961
(1.00) 		0.081
(1.00) 		0.0669
(1.00) 		0.0621
(1.00) 		0.424
(1.00) 		0.00145
(1.00) 		0.275
(1.00) 		0.799
(1.00) 		0.0283
(1.00) 		0.00197
(1.00) 		0.726
(1.00) 		0.000395
(0.357) 		0.568
(1.00)
del 5q22 2 178 (30%) 414 0.101
(1.00) 		0.482
(1.00) 		0.0857
(1.00) 		0.0645
(1.00) 		0.753
(1.00) 		0.0188
(1.00) 		0.0304
(1.00) 		0.473
(1.00) 		0.0297
(1.00) 		0.000398
(0.359) 		0.231
(1.00) 		0.0157
(1.00) 		0.284
(1.00)
del 6p25 3 78 (13%) 514 0.132
(1.00) 		0.0853
(1.00) 		0.889
(1.00) 		0.522
(1.00) 		0.412
(1.00) 		0.478
(1.00) 		0.28
(1.00) 		0.0877
(1.00) 		0.551
(1.00) 		0.337
(1.00) 		0.38
(1.00) 		0.484
(1.00) 		0.0161
(1.00)
del 6q26 90 (15%) 502 0.0323
(1.00) 		0.71
(1.00) 		0.298
(1.00) 		0.147
(1.00) 		0.143
(1.00) 		0.00417
(1.00) 		0.0413
(1.00) 		0.253
(1.00) 		0.0372
(1.00) 		0.632
(1.00) 		0.156
(1.00) 		0.00302
(1.00) 		0.0237
(1.00)
del 7q31 1 16 (3%) 576 0.987
(1.00) 		0.512
(1.00) 		1
(1.00) 		0.714
(1.00) 		0.512
(1.00) 		0.887
(1.00) 		0.102
(1.00) 		0.459
(1.00) 		0.505
(1.00) 		1
(1.00) 		0.738
(1.00) 		0.713
(1.00) 		0.574
(1.00)
del 8p11 21 128 (22%) 464 0.483
(1.00) 		0.168
(1.00) 		0.0324
(1.00) 		0.0961
(1.00) 		0.364
(1.00) 		0.0103
(1.00) 		0.055
(1.00) 		0.55
(1.00) 		0.164
(1.00) 		0.415
(1.00) 		0.0832
(1.00) 		0.0203
(1.00) 		0.0793
(1.00)
del 8q11 1 46 (8%) 546 0.354
(1.00) 		0.362
(1.00) 		0.22
(1.00) 		0.127
(1.00) 		0.687
(1.00) 		0.0762
(1.00) 		0.0268
(1.00) 		0.287
(1.00) 		0.47
(1.00) 		0.52
(1.00) 		0.345
(1.00) 		0.0394
(1.00) 		0.0688
(1.00)
del 9p24 2 81 (14%) 511 0.241
(1.00) 		0.103
(1.00) 		0.416
(1.00) 		0.685
(1.00) 		0.384
(1.00) 		0.165
(1.00) 		0.0479
(1.00) 		0.0412
(1.00) 		0.182
(1.00) 		0.355
(1.00) 		0.119
(1.00) 		0.0448
(1.00) 		0.775
(1.00)
del 10q21 1 126 (21%) 466 0.633
(1.00) 		0.0384
(1.00) 		0.65
(1.00) 		0.33
(1.00) 		0.717
(1.00) 		0.252
(1.00) 		0.615
(1.00) 		1
(1.00) 		0.096
(1.00) 		0.0244
(1.00) 		0.466
(1.00) 		0.101
(1.00) 		0.709
(1.00)
del 10q23 31 153 (26%) 439 0.658
(1.00) 		0.00636
(1.00) 		0.0712
(1.00) 		0.109
(1.00) 		0.604
(1.00) 		0.0832
(1.00) 		0.0817
(1.00) 		0.925
(1.00) 		0.0114
(1.00) 		0.0113
(1.00) 		0.626
(1.00) 		0.0235
(1.00) 		0.901
(1.00)
del 10q25 2 150 (25%) 442 0.259
(1.00) 		0.0526
(1.00) 		0.241
(1.00) 		0.243
(1.00) 		0.311
(1.00) 		0.034
(1.00) 		0.237
(1.00) 		1
(1.00) 		0.0311
(1.00) 		0.0102
(1.00) 		0.593
(1.00) 		0.0221
(1.00) 		1
(1.00)
del 11q22 3 109 (18%) 483 0.356
(1.00) 		0.509
(1.00) 		0.0698
(1.00) 		0.796
(1.00) 		0.788
(1.00) 		0.251
(1.00) 		0.53
(1.00) 		0.526
(1.00) 		0.0489
(1.00) 		0.22
(1.00) 		0.651
(1.00) 		0.0869
(1.00) 		0.347
(1.00)
del 12p13 1 86 (15%) 506 0.0637
(1.00) 		0.333
(1.00) 		0.0844
(1.00) 		0.263
(1.00) 		0.475
(1.00) 		0.0195
(1.00) 		0.0994
(1.00) 		0.726
(1.00) 		0.00531
(1.00) 		0.626
(1.00) 		0.837
(1.00) 		0.071
(1.00) 		0.681
(1.00)
del 12q21 33 85 (14%) 507 0.17
(1.00) 		0.713
(1.00) 		0.288
(1.00) 		0.0381
(1.00) 		0.509
(1.00) 		0.15
(1.00) 		0.315
(1.00) 		0.907
(1.00) 		0.0419
(1.00) 		0.624
(1.00) 		0.613
(1.00) 		0.0518
(1.00) 		0.754
(1.00)
del 15q11 2 240 (41%) 352 0.93
(1.00) 		0.485
(1.00) 		0.156
(1.00) 		0.175
(1.00) 		0.735
(1.00) 		0.0194
(1.00) 		0.195
(1.00) 		0.402
(1.00) 		0.0364
(1.00) 		0.0351
(1.00) 		0.756
(1.00) 		0.00655
(1.00) 		0.0949
(1.00)
del 15q15 2 237 (40%) 355 0.969
(1.00) 		0.31
(1.00) 		0.0292
(1.00) 		0.104
(1.00) 		0.696
(1.00) 		0.00415
(1.00) 		0.0505
(1.00) 		0.275
(1.00) 		0.00805
(1.00) 		0.0339
(1.00) 		0.471
(1.00) 		0.00328
(1.00) 		0.0822
(1.00)
del 15q21 1 235 (40%) 357 0.66
(1.00) 		0.597
(1.00) 		0.0288
(1.00) 		0.213
(1.00) 		0.787
(1.00) 		0.0231
(1.00) 		0.0795
(1.00) 		0.207
(1.00) 		0.00837
(1.00) 		0.0332
(1.00) 		0.409
(1.00) 		0.0143
(1.00) 		0.0212
(1.00)
del 15q22 33 225 (38%) 367 0.757
(1.00) 		0.327
(1.00) 		0.00959
(1.00) 		0.0156
(1.00) 		0.0705
(1.00) 		0.00508
(1.00) 		0.0555
(1.00) 		0.498
(1.00) 		0.00351
(1.00) 		0.00243
(1.00) 		0.519
(1.00) 		0.00214
(1.00) 		0.0169
(1.00)
del 16p13 3 65 (11%) 527 0.00218
(1.00) 		0.937
(1.00) 		0.187
(1.00) 		0.0114
(1.00) 		0.0598
(1.00) 		0.196
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.272
(1.00) 		0.607
(1.00) 		0.482
(1.00) 		0.127
(1.00) 		0.289
(1.00)
del 16q23 1 79 (13%) 513 0.0151
(1.00) 		0.536
(1.00) 		0.683
(1.00) 		0.304
(1.00) 		0.222
(1.00) 		0.617
(1.00) 		0.673
(1.00) 		0.228
(1.00) 		0.771
(1.00) 		1
(1.00) 		0.847
(1.00) 		0.959
(1.00) 		0.303
(1.00)
del 17q24 3 89 (15%) 503 0.0918
(1.00) 		0.332
(1.00) 		1
(1.00) 		0.0355
(1.00) 		0.187
(1.00) 		0.00475
(1.00) 		0.0615
(1.00) 		0.135
(1.00) 		1
(1.00) 		0.631
(1.00) 		0.433
(1.00) 		0.000411
(0.37) 		0.126
(1.00)
del 20p12 1 181 (31%) 411 0.0486
(1.00) 		0.651
(1.00) 		0.0274
(1.00) 		0.187
(1.00) 		0.428
(1.00) 		0.23
(1.00) 		0.598
(1.00) 		0.372
(1.00) 		0.0996
(1.00) 		0.0633
(1.00) 		0.363
(1.00) 		0.395
(1.00) 		0.0179
(1.00)
del 20p12 1 181 (31%) 411 0.0486
(1.00) 		0.651
(1.00) 		0.0274
(1.00) 		0.185
(1.00) 		0.43
(1.00) 		0.23
(1.00) 		0.602
(1.00) 		0.372
(1.00) 		0.102
(1.00) 		0.0633
(1.00) 		0.369
(1.00) 		0.395
(1.00) 		0.018
(1.00)
del 21q11 2 206 (35%) 386 0.334
(1.00) 		0.71
(1.00) 		0.00638
(1.00) 		0.295
(1.00) 		0.904
(1.00) 		0.0334
(1.00) 		0.343
(1.00) 		0.604
(1.00) 		0.00034
(0.308) 		0.288
(1.00) 		0.728
(1.00) 		0.00477
(1.00) 		0.649
(1.00)
del 22q13 32 218 (37%) 374 0.0283
(1.00) 		0.815
(1.00) 		0.21
(1.00) 		0.0105
(1.00) 		0.359
(1.00) 		0.00052
(0.467) 		0.0146
(1.00) 		0.442
(1.00) 		0.00422
(1.00) 		0.731
(1.00) 		0.428
(1.00) 		0.00039
(0.353) 		0.617
(1.00)
'amp_6p21.1' versus 'PATHOLOGY.N.STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.19

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

nPatients N0 N1 N2
ALL 335 146 108
AMP PEAK 5(6P21.1) MUTATED 65 40 42
AMP PEAK 5(6P21.1) WILD-TYPE 270 106 66

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

'amp_13q12.13' versus 'NEOPLASM.DISEASESTAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.047

Table S2.  Gene #13: '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 36 165 10 3 26 22 76 52 60 25 1
AMP PEAK 13(13Q12.13) MUTATED 63 0 16 94 4 3 15 17 56 37 49 22 0
AMP PEAK 13(13Q12.13) WILD-TYPE 39 1 20 71 6 0 11 5 20 15 11 3 1

Figure S2.  Get High-res Image Gene #13: 'amp_13q12.13' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

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

P value = 4e-05 (Fisher's exact test), Q value = 0.037

Table S3.  Gene #13: 'amp_13q12.13' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
AMP PEAK 13(13Q12.13) MUTATED 190 111 81
AMP PEAK 13(13Q12.13) WILD-TYPE 145 35 27

Figure S3.  Get High-res Image Gene #13: '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 = 0.0096

Table S4.  Gene #13: 'amp_13q12.13' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
AMP PEAK 13(13Q12.13) MUTATED 244 16 114 5
AMP PEAK 13(13Q12.13) WILD-TYPE 129 39 29 8

Figure S4.  Get High-res Image Gene #13: 'amp_13q12.13' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 0.000111 (Wilcoxon-test), Q value = 0.1

Table S5.  Gene #13: 'amp_13q12.13' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
AMP PEAK 13(13Q12.13) MUTATED 366 2.5 (4.9)
AMP PEAK 13(13Q12.13) WILD-TYPE 192 1.6 (4.2)

Figure S5.  Get High-res Image Gene #13: 'amp_13q12.13' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'amp_13q12.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.23

Table S6.  Gene #14: '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 36 165 10 3 26 22 76 52 60 25 1
AMP PEAK 14(13Q12.2) MUTATED 63 0 16 92 4 3 15 17 56 36 48 21 0
AMP PEAK 14(13Q12.2) WILD-TYPE 39 1 20 73 6 0 11 5 20 16 12 4 1

Figure S6.  Get High-res Image Gene #14: 'amp_13q12.2' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

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

P value = 5e-05 (Fisher's exact test), Q value = 0.047

Table S7.  Gene #14: 'amp_13q12.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
AMP PEAK 14(13Q12.2) MUTATED 188 109 80
AMP PEAK 14(13Q12.2) WILD-TYPE 147 37 28

Figure S7.  Get High-res Image Gene #14: '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 = 0.0096

Table S8.  Gene #14: 'amp_13q12.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
AMP PEAK 14(13Q12.2) MUTATED 240 16 113 5
AMP PEAK 14(13Q12.2) WILD-TYPE 133 39 30 8

Figure S8.  Get High-res Image Gene #14: 'amp_13q12.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 0.000139 (Wilcoxon-test), Q value = 0.13

Table S9.  Gene #14: 'amp_13q12.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
AMP PEAK 14(13Q12.2) MUTATED 362 2.5 (4.9)
AMP PEAK 14(13Q12.2) WILD-TYPE 196 1.7 (4.2)

Figure S9.  Get High-res Image Gene #14: '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 = 0.028

Table S10.  Gene #15: 'amp_13q22.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
AMP PEAK 15(13Q22.1) MUTATED 190 110 79
AMP PEAK 15(13Q22.1) WILD-TYPE 145 36 29

Figure S10.  Get High-res Image Gene #15: '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 = 0.0096

Table S11.  Gene #15: 'amp_13q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
AMP PEAK 15(13Q22.1) MUTATED 246 18 109 4
AMP PEAK 15(13Q22.1) WILD-TYPE 127 37 34 9

Figure S11.  Get High-res Image Gene #15: 'amp_13q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 5e-05 (Fisher's exact test), Q value = 0.047

Table S12.  Gene #17: 'amp_16p11.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
AMP PEAK 17(16P11.2) MUTATED 69 54 41
AMP PEAK 17(16P11.2) WILD-TYPE 266 92 67

Figure S12.  Get High-res Image Gene #17: 'amp_16p11.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

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

P value = 6.58e-05 (Wilcoxon-test), Q value = 0.061

Table S13.  Gene #17: 'amp_16p11.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
AMP PEAK 17(16P11.2) MUTATED 157 3.1 (6.0)
AMP PEAK 17(16P11.2) WILD-TYPE 401 1.8 (4.1)

Figure S13.  Get High-res Image Gene #17: 'amp_16p11.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'amp_20p11.23' versus 'PATHOLOGY.M.STAGE'

P value = 0.00027 (Fisher's exact test), Q value = 0.25

Table S14.  Gene #22: 'amp_20p11.23' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 443 72 9 1 58
AMP PEAK 22(20P11.23) MUTATED 215 48 9 0 35
AMP PEAK 22(20P11.23) WILD-TYPE 228 24 0 1 23

Figure S14.  Get High-res Image Gene #22: 'amp_20p11.23' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

'amp_20p11.21' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S15.  Gene #23: 'amp_20p11.21' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
AMP PEAK 23(20P11.21) MUTATED 218 20 103 4
AMP PEAK 23(20P11.21) WILD-TYPE 155 35 40 9

Figure S15.  Get High-res Image Gene #23: 'amp_20p11.21' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 6.64e-06 (Fisher's exact test), Q value = 0.0064

Table S16.  Gene #24: 'amp_20q11.21' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 429 159
AMP PEAK 24(20Q11.21) MUTATED 306 141
AMP PEAK 24(20Q11.21) WILD-TYPE 123 18

Figure S16.  Get High-res Image Gene #24: '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 = 0.0096

Table S17.  Gene #24: 'amp_20q11.21' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
AMP PEAK 24(20Q11.21) MUTATED 281 24 132 7
AMP PEAK 24(20Q11.21) WILD-TYPE 92 31 11 6

Figure S17.  Get High-res Image Gene #24: 'amp_20q11.21' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 3.44e-06 (Fisher's exact test), Q value = 0.0033

Table S18.  Gene #25: 'amp_20q12' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 429 159
AMP PEAK 25(20Q12) MUTATED 307 142
AMP PEAK 25(20Q12) WILD-TYPE 122 17

Figure S18.  Get High-res Image Gene #25: 'amp_20q12' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'amp_20q12' versus 'NEOPLASM.DISEASESTAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.056

Table S19.  Gene #25: '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 36 165 10 3 26 22 76 52 60 25 1
AMP PEAK 25(20Q12) MUTATED 77 1 21 114 5 3 18 21 60 43 54 24 0
AMP PEAK 25(20Q12) WILD-TYPE 25 0 15 51 5 0 8 1 16 9 6 1 1

Figure S19.  Get High-res Image Gene #25: 'amp_20q12' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'amp_20q12' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S20.  Gene #25: 'amp_20q12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
AMP PEAK 25(20Q12) MUTATED 283 23 133 7
AMP PEAK 25(20Q12) WILD-TYPE 90 32 10 6

Figure S20.  Get High-res Image Gene #25: 'amp_20q12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 5.34e-06 (Fisher's exact test), Q value = 0.0052

Table S21.  Gene #26: 'amp_20q13.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 429 159
AMP PEAK 26(20Q13.31) MUTATED 309 142
AMP PEAK 26(20Q13.31) WILD-TYPE 120 17

Figure S21.  Get High-res Image Gene #26: 'amp_20q13.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'amp_20q13.31' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.15

Table S22.  Gene #26: 'amp_20q13.31' 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 36 165 10 3 26 22 76 52 60 25 1
AMP PEAK 26(20Q13.31) MUTATED 77 1 22 115 5 3 19 21 60 44 55 23 0
AMP PEAK 26(20Q13.31) WILD-TYPE 25 0 14 50 5 0 7 1 16 8 5 2 1

Figure S22.  Get High-res Image Gene #26: 'amp_20q13.31' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'amp_20q13.31' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S23.  Gene #26: 'amp_20q13.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
AMP PEAK 26(20Q13.31) MUTATED 284 24 133 7
AMP PEAK 26(20Q13.31) WILD-TYPE 89 31 10 6

Figure S23.  Get High-res Image Gene #26: 'amp_20q13.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 2e-04 (Fisher's exact test), Q value = 0.18

Table S24.  Gene #28: 'del_1p36.11' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 443 72 9 1 58
DEL PEAK 1(1P36.11) MUTATED 157 45 5 0 24
DEL PEAK 1(1P36.11) WILD-TYPE 286 27 4 1 34

Figure S24.  Get High-res Image Gene #28: 'del_1p36.11' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

'del_1p36.11' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000259 (Wilcoxon-test), Q value = 0.24

Table S25.  Gene #28: 'del_1p36.11' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
DEL PEAK 1(1P36.11) MUTATED 220 3.1 (6.0)
DEL PEAK 1(1P36.11) WILD-TYPE 338 1.6 (3.5)

Figure S25.  Get High-res Image Gene #28: 'del_1p36.11' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_4p16.1' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.17e-05 (Fisher's exact test), Q value = 0.03

Table S26.  Gene #37: 'del_4p16.1' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients NO YES
ALL 9 583
DEL PEAK 10(4P16.1) MUTATED 9 181
DEL PEAK 10(4P16.1) WILD-TYPE 0 402

Figure S26.  Get High-res Image Gene #37: 'del_4p16.1' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'del_4p16.1' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000257 (Wilcoxon-test), Q value = 0.23

Table S27.  Gene #37: 'del_4p16.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
DEL PEAK 10(4P16.1) MUTATED 182 3.1 (5.5)
DEL PEAK 10(4P16.1) WILD-TYPE 376 1.7 (4.2)

Figure S27.  Get High-res Image Gene #37: 'del_4p16.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_5q11.2' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 8.86e-05 (Fisher's exact test), Q value = 0.082

Table S28.  Gene #40: 'del_5q11.2' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients NO YES
ALL 9 583
DEL PEAK 13(5Q11.2) MUTATED 8 139
DEL PEAK 13(5Q11.2) WILD-TYPE 1 444

Figure S28.  Get High-res Image Gene #40: 'del_5q11.2' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

P value = 3.96e-05 (Fisher's exact test), Q value = 0.037

Table S29.  Gene #45: 'del_8p23.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 429 159
DEL PEAK 18(8P23.2) MUTATED 179 97
DEL PEAK 18(8P23.2) WILD-TYPE 250 62

Figure S29.  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 = 0.00017 (Fisher's exact test), Q value = 0.16

Table S30.  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 36 165 10 3 26 22 76 52 60 25 1
DEL PEAK 18(8P23.2) MUTATED 39 0 12 64 3 2 14 11 40 32 43 12 1
DEL PEAK 18(8P23.2) WILD-TYPE 63 1 24 101 7 1 12 11 36 20 17 13 0

Figure S30.  Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

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

P value = 5e-05 (Fisher's exact test), Q value = 0.047

Table S31.  Gene #45: 'del_8p23.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
DEL PEAK 18(8P23.2) MUTATED 130 78 68
DEL PEAK 18(8P23.2) WILD-TYPE 205 68 40

Figure S31.  Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_8p23.2' versus 'HISTOLOGICAL.TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.028

Table S32.  Gene #45: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
DEL PEAK 18(8P23.2) MUTATED 163 15 88 7
DEL PEAK 18(8P23.2) WILD-TYPE 210 40 55 6

Figure S32.  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 = 1.86e-05 (Wilcoxon-test), Q value = 0.018

Table S33.  Gene #45: 'del_8p23.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
DEL PEAK 18(8P23.2) MUTATED 266 2.9 (5.8)
DEL PEAK 18(8P23.2) WILD-TYPE 292 1.5 (3.4)

Figure S33.  Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

'del_8p22' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S34.  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 36 165 10 3 26 22 76 52 60 25 1
DEL PEAK 19(8P22) MUTATED 39 0 13 66 3 2 14 13 43 35 43 15 1
DEL PEAK 19(8P22) WILD-TYPE 63 1 23 99 7 1 12 9 33 17 17 10 0

Figure S34.  Get High-res Image Gene #46: 'del_8p22' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

'del_8p22' versus 'PATHOLOGY.N.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S35.  Gene #46: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
DEL PEAK 19(8P22) MUTATED 134 82 74
DEL PEAK 19(8P22) WILD-TYPE 201 64 34

Figure S35.  Get High-res Image Gene #46: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_8p22' versus 'HISTOLOGICAL.TYPE'

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

Table S36.  Gene #46: 'del_8p22' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
DEL PEAK 19(8P22) MUTATED 175 16 89 7
DEL PEAK 19(8P22) WILD-TYPE 198 39 54 6

Figure S36.  Get High-res Image Gene #46: 'del_8p22' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 3.88e-07 (Wilcoxon-test), Q value = 0.00038

Table S37.  Gene #46: 'del_8p22' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
DEL PEAK 19(8P22) MUTATED 280 3.0 (5.7)
DEL PEAK 19(8P22) WILD-TYPE 278 1.4 (3.3)

Figure S37.  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 = 0.0096

Table S38.  Gene #56: 'del_14q11.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
DEL PEAK 29(14Q11.2) MUTATED 125 5 64 2
DEL PEAK 29(14Q11.2) WILD-TYPE 248 50 79 11

Figure S38.  Get High-res Image Gene #56: 'del_14q11.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_14q31.1' versus 'HISTOLOGICAL.TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S39.  Gene #57: 'del_14q31.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
DEL PEAK 30(14Q31.1) MUTATED 132 5 64 1
DEL PEAK 30(14Q31.1) WILD-TYPE 241 50 79 12

Figure S39.  Get High-res Image Gene #57: 'del_14q31.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_14q31.1' versus 'HISTOLOGICAL.TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S40.  Gene #58: 'del_14q31.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
DEL PEAK 31(14Q31.1) MUTATED 134 5 63 1
DEL PEAK 31(14Q31.1) WILD-TYPE 239 50 80 12

Figure S40.  Get High-res Image Gene #58: 'del_14q31.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

'del_17p12' versus 'PATHOLOGY.N.STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.084

Table S41.  Gene #65: 'del_17p12' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
DEL PEAK 38(17P12) MUTATED 174 99 78
DEL PEAK 38(17P12) WILD-TYPE 161 47 30

Figure S41.  Get High-res Image Gene #65: 'del_17p12' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_17p12' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S42.  Gene #65: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
DEL PEAK 38(17P12) MUTATED 223 14 103 6
DEL PEAK 38(17P12) WILD-TYPE 150 41 40 7

Figure S42.  Get High-res Image Gene #65: 'del_17p12' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 1.86e-05 (Wilcoxon-test), Q value = 0.018

Table S43.  Gene #65: 'del_17p12' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
DEL PEAK 38(17P12) MUTATED 333 2.6 (5.2)
DEL PEAK 38(17P12) WILD-TYPE 225 1.5 (3.8)

Figure S43.  Get High-res Image Gene #65: 'del_17p12' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

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

P value = 3.13e-06 (Fisher's exact test), Q value = 0.003

Table S44.  Gene #67: 'del_18p11.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 429 159
DEL PEAK 40(18P11.31) MUTATED 230 119
DEL PEAK 40(18P11.31) WILD-TYPE 199 40

Figure S44.  Get High-res Image Gene #67: 'del_18p11.31' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'del_18p11.31' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00024 (Fisher's exact test), Q value = 0.22

Table S45.  Gene #67: '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 36 165 10 3 26 22 76 52 60 25 1
DEL PEAK 40(18P11.31) MUTATED 56 0 14 91 4 3 12 14 49 33 46 22 0
DEL PEAK 40(18P11.31) WILD-TYPE 46 1 22 74 6 0 14 8 27 19 14 3 1

Figure S45.  Get High-res Image Gene #67: '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 = 0.028

Table S46.  Gene #67: 'del_18p11.31' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 443 72 9 1 58
DEL PEAK 40(18P11.31) MUTATED 250 58 9 0 31
DEL PEAK 40(18P11.31) WILD-TYPE 193 14 0 1 27

Figure S46.  Get High-res Image Gene #67: '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 = 0.0096

Table S47.  Gene #67: 'del_18p11.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
DEL PEAK 40(18P11.31) MUTATED 222 7 113 6
DEL PEAK 40(18P11.31) WILD-TYPE 151 48 30 7

Figure S47.  Get High-res Image Gene #67: 'del_18p11.31' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 1.14e-09 (Fisher's exact test), Q value = 1.1e-06

Table S48.  Gene #68: 'del_18q12.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 429 159
DEL PEAK 41(18Q12.2) MUTATED 257 136
DEL PEAK 41(18Q12.2) WILD-TYPE 172 23

Figure S48.  Get High-res Image Gene #68: 'del_18q12.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 0.00015 (Fisher's exact test), Q value = 0.14

Table S49.  Gene #68: 'del_18q12.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
DEL PEAK 41(18Q12.2) MUTATED 200 112 81
DEL PEAK 41(18Q12.2) WILD-TYPE 135 34 27

Figure S49.  Get High-res Image Gene #68: '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 = 0.0096

Table S50.  Gene #68: 'del_18q12.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
DEL PEAK 41(18Q12.2) MUTATED 245 11 125 10
DEL PEAK 41(18Q12.2) WILD-TYPE 128 44 18 3

Figure S50.  Get High-res Image Gene #68: 'del_18q12.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

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

Table S51.  Gene #69: 'del_18q21.2' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 429 159
DEL PEAK 42(18Q21.2) MUTATED 271 140
DEL PEAK 42(18Q21.2) WILD-TYPE 158 19

Figure S51.  Get High-res Image Gene #69: '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 = 0.0096

Table S52.  Gene #69: '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 36 165 10 3 26 22 76 52 60 25 1
DEL PEAK 42(18Q21.2) MUTATED 61 0 23 102 4 3 16 18 59 42 54 22 1
DEL PEAK 42(18Q21.2) WILD-TYPE 41 1 13 63 6 0 10 4 17 10 6 3 0

Figure S52.  Get High-res Image Gene #69: 'del_18q21.2' versus Clinical Feature #4: 'NEOPLASM.DISEASESTAGE'

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

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S53.  Gene #69: 'del_18q21.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
DEL PEAK 42(18Q21.2) MUTATED 206 116 89
DEL PEAK 42(18Q21.2) WILD-TYPE 129 30 19

Figure S53.  Get High-res Image Gene #69: 'del_18q21.2' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

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

P value = 0.00019 (Fisher's exact test), Q value = 0.17

Table S54.  Gene #69: 'del_18q21.2' versus Clinical Feature #7: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 M1A M1B MX
ALL 443 72 9 1 58
DEL PEAK 42(18Q21.2) MUTATED 298 65 8 1 38
DEL PEAK 42(18Q21.2) WILD-TYPE 145 7 1 0 20

Figure S54.  Get High-res Image Gene #69: '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 = 0.0096

Table S55.  Gene #69: 'del_18q21.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
DEL PEAK 42(18Q21.2) MUTATED 256 14 126 12
DEL PEAK 42(18Q21.2) WILD-TYPE 117 41 17 1

Figure S55.  Get High-res Image Gene #69: 'del_18q21.2' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 2.2e-06 (Wilcoxon-test), Q value = 0.0021

Table S56.  Gene #69: 'del_18q21.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
DEL PEAK 42(18Q21.2) MUTATED 391 2.5 (5.0)
DEL PEAK 42(18Q21.2) WILD-TYPE 167 1.4 (3.9)

Figure S56.  Get High-res Image Gene #69: 'del_18q21.2' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

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

P value = 2.25e-07 (Fisher's exact test), Q value = 0.00022

Table S57.  Gene #70: 'del_18q22.1' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients COLON RECTUM
ALL 429 159
DEL PEAK 43(18Q22.1) MUTATED 271 135
DEL PEAK 43(18Q22.1) WILD-TYPE 158 24

Figure S57.  Get High-res Image Gene #70: 'del_18q22.1' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'del_18q22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.019

Table S58.  Gene #70: '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 36 165 10 3 26 22 76 52 60 25 1
DEL PEAK 43(18Q22.1) MUTATED 61 0 23 102 4 3 14 17 58 42 53 22 1
DEL PEAK 43(18Q22.1) WILD-TYPE 41 1 13 63 6 0 12 5 18 10 7 3 0

Figure S58.  Get High-res Image Gene #70: '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 = 0.019

Table S59.  Gene #70: 'del_18q22.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
DEL PEAK 43(18Q22.1) MUTATED 206 112 88
DEL PEAK 43(18Q22.1) WILD-TYPE 129 34 20

Figure S59.  Get High-res Image Gene #70: 'del_18q22.1' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

'del_18q22.1' versus 'HISTOLOGICAL.TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S60.  Gene #70: 'del_18q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 373 55 143 13
DEL PEAK 43(18Q22.1) MUTATED 257 13 124 10
DEL PEAK 43(18Q22.1) WILD-TYPE 116 42 19 3

Figure S60.  Get High-res Image Gene #70: 'del_18q22.1' versus Clinical Feature #9: 'HISTOLOGICAL.TYPE'

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

P value = 2.73e-05 (Wilcoxon-test), Q value = 0.026

Table S61.  Gene #70: 'del_18q22.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
DEL PEAK 43(18Q22.1) MUTATED 388 2.5 (5.0)
DEL PEAK 43(18Q22.1) WILD-TYPE 170 1.4 (3.8)

Figure S61.  Get High-res Image Gene #70: 'del_18q22.1' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

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

P value = 0.00018 (Fisher's exact test), Q value = 0.17

Table S62.  Gene #71: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 335 146 108
DEL PEAK 44(19P13.3) MUTATED 36 27 30
DEL PEAK 44(19P13.3) WILD-TYPE 299 119 78

Figure S62.  Get High-res Image Gene #71: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY.N.STAGE'

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

P value = 3.4e-06 (Wilcoxon-test), Q value = 0.0033

Table S63.  Gene #71: 'del_19p13.3' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 558 2.2 (4.7)
DEL PEAK 44(19P13.3) MUTATED 88 3.9 (6.0)
DEL PEAK 44(19P13.3) WILD-TYPE 470 1.9 (4.4)

Figure S63.  Get High-res Image Gene #71: 'del_19p13.3' 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 = 592

  • Number of significantly focal cnvs = 75

  • 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.

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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