Correlation between copy number variations of arm-level result and selected clinical features
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 82 arm-level events and 13 clinical features across 614 patients, 210 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 2p gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RESIDUAL_TUMOR'.

  • 2q gain cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 3p gain cnv correlated to 'TUMOR_TISSUE_SITE' and 'PATHOLOGIC_STAGE'.

  • 3q gain cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 4q gain cnv correlated to 'PATHOLOGY_M_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 5p gain cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 5q gain cnv correlated to 'TUMOR_TISSUE_SITE' and 'HISTOLOGICAL_TYPE'.

  • 6p gain cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 6q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 7p gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 7q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 8q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 9p gain cnv correlated to 'Time to Death',  'TUMOR_TISSUE_SITE', and 'HISTOLOGICAL_TYPE'.

  • 9q gain cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • 10p gain cnv correlated to 'Time to Death' and 'PATHOLOGY_N_STAGE'.

  • 10q gain cnv correlated to 'ETHNICITY'.

  • 11p gain cnv correlated to 'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 11q gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 12q gain cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 13q gain cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 16p gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 16q gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 17p gain cnv correlated to 'Time to Death'.

  • 17q gain cnv correlated to 'PATHOLOGY_M_STAGE'.

  • 18p gain cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 18q gain cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.

  • 20p gain cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 20q gain cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RESIDUAL_TUMOR', and 'NUMBER_OF_LYMPH_NODES'.

  • 21q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 1p loss cnv correlated to 'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 1q loss cnv correlated to 'PATHOLOGY_M_STAGE' and 'GENDER'.

  • 2p loss cnv correlated to 'TUMOR_TISSUE_SITE' and 'HISTOLOGICAL_TYPE'.

  • 3p loss cnv correlated to 'Time to Death',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 3q loss cnv correlated to 'PATHOLOGY_M_STAGE' and 'HISTOLOGICAL_TYPE'.

  • 4p loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 4q loss cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 5p loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'ETHNICITY'.

  • 5q loss cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 6p loss cnv correlated to 'Time to Death' and 'RADIATION_THERAPY'.

  • 6q loss cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.

  • 7p loss cnv correlated to 'ETHNICITY'.

  • 7q loss cnv correlated to 'ETHNICITY'.

  • 8p loss cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 9p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'RESIDUAL_TUMOR'.

  • 9q loss cnv correlated to 'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • 10p loss cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 10q loss cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • 11p loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 11q loss cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 12p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'NUMBER_OF_LYMPH_NODES'.

  • 12q loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 13q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'NUMBER_OF_LYMPH_NODES'.

  • 14q loss cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 15q loss cnv correlated to 'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 17p loss cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 17q loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 18p loss cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 18q loss cnv correlated to 'YEARS_TO_BIRTH',  'TUMOR_TISSUE_SITE',  'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 19p loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 19q loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 21q loss cnv correlated to 'TUMOR_TISSUE_SITE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'ETHNICITY'.

  • 22q loss cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • xp loss cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • xq loss cnv correlated to 'PATHOLOGY_M_STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 210 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		TUMOR
TISSUE
SITE 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		ETHNICITY
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
20q gain 461 (75%) 153 0.949
(1.00) 		0.4
(0.747) 		2.56e-06
(0.000888) 		0.00036
(0.0128) 		0.0961
(0.374) 		0.0006
(0.0173) 		0.00111
(0.0232) 		0.224
(0.583) 		0.505
(0.823) 		1e-05
(0.000888) 		0.0349
(0.206) 		0.00345
(0.049) 		1
(1.00)
18q loss 407 (66%) 207 0.582
(0.862) 		0.0326
(0.197) 		4.06e-08
(4.32e-05) 		0.00011
(0.00533) 		0.367
(0.712) 		0.00023
(0.00876) 		5.81e-05
(0.00387) 		0.348
(0.692) 		1
(1.00) 		1e-05
(0.000888) 		0.0829
(0.336) 		0.000441
(0.0144) 		1
(1.00)
13q gain 372 (61%) 242 0.61
(0.877) 		0.634
(0.889) 		0.0147
(0.128) 		0.00072
(0.0183) 		0.785
(0.966) 		0.00011
(0.00533) 		0.0121
(0.117) 		0.248
(0.608) 		0.166
(0.503) 		1e-05
(0.000888) 		0.0717
(0.306) 		0.000647
(0.0177) 		0.654
(0.898)
20p gain 352 (57%) 262 0.531
(0.834) 		0.913
(1.00) 		0.00545
(0.0717) 		0.00096
(0.0213) 		0.447
(0.788) 		0.0222
(0.156) 		0.000901
(0.0209) 		0.121
(0.432) 		0.446
(0.787) 		2e-05
(0.00142) 		0.0658
(0.292) 		0.0199
(0.147) 		0.656
(0.898)
3p loss 67 (11%) 547 0.031
(0.19) 		0.957
(1.00) 		0.237
(0.602) 		0.106
(0.395) 		0.0488
(0.249) 		0.0194
(0.147) 		0.00101
(0.0219) 		0.368
(0.712) 		1
(1.00) 		0.0353
(0.206) 		0.169
(0.503) 		0.0146
(0.128) 		0.45
(0.788)
8p loss 215 (35%) 399 0.204
(0.552) 		0.718
(0.923) 		0.00204
(0.0339) 		0.00912
(0.0972) 		0.517
(0.827) 		0.00013
(0.00603) 		0.00232
(0.0364) 		0.128
(0.439) 		0.55
(0.845) 		0.00143
(0.0288) 		0.0672
(0.295) 		1.86e-05
(0.00142) 		0.0576
(0.271)
17p loss 338 (55%) 276 0.142
(0.46) 		0.42
(0.757) 		0.027
(0.177) 		0.00208
(0.0339) 		0.343
(0.69) 		0.00109
(0.0232) 		0.00221
(0.0351) 		0.194
(0.54) 		1
(1.00) 		1e-05
(0.000888) 		0.103
(0.388) 		0.00047
(0.0147) 		1
(1.00)
18p loss 380 (62%) 234 0.397
(0.745) 		0.0553
(0.271) 		7.77e-07
(0.000414) 		8e-05
(0.00449) 		0.867
(1.00) 		0.00317
(0.0469) 		1.11e-05
(0.000913) 		0.36
(0.705) 		0.556
(0.847) 		1e-05
(0.000888) 		0.0574
(0.271) 		0.0028
(0.042) 		0.654
(0.898)
7p gain 348 (57%) 266 0.784
(0.966) 		0.223
(0.583) 		0.0647
(0.29) 		0.00015
(0.00666) 		0.892
(1.00) 		1e-05
(0.000888) 		0.0193
(0.147) 		0.568
(0.852) 		0.7
(0.918) 		0.00026
(0.00956) 		0.324
(0.681) 		7.06e-05
(0.00443) 		0.4
(0.747)
7q gain 311 (51%) 303 0.975
(1.00) 		0.177
(0.514) 		0.521
(0.828) 		0.00011
(0.00533) 		0.633
(0.889) 		0.00072
(0.0183) 		0.00743
(0.0861) 		0.628
(0.889) 		0.85
(0.991) 		0.00326
(0.0471) 		0.477
(0.809) 		0.00189
(0.0336) 		0.672
(0.905)
4p loss 195 (32%) 419 0.508
(0.823) 		0.92
(1.00) 		0.2
(0.549) 		0.00638
(0.0769) 		0.768
(0.955) 		0.00183
(0.0331) 		0.000626
(0.0176) 		0.664
(0.902) 		0.0642
(0.29) 		0.0187
(0.147) 		0.344
(0.691) 		0.000718
(0.0183) 		0.169
(0.503)
5q loss 120 (20%) 494 0.0344
(0.205) 		0.805
(0.972) 		0.0656
(0.292) 		0.0372
(0.211) 		0.661
(0.902) 		0.0147
(0.128) 		0.0377
(0.211) 		0.541
(0.837) 		0.48
(0.812) 		0.0575
(0.271) 		0.234
(0.601) 		0.0058
(0.0744) 		0.0579
(0.271)
21q loss 192 (31%) 422 0.844
(0.988) 		0.477
(0.809) 		0.00156
(0.0297) 		0.287
(0.648) 		0.896
(1.00) 		0.0139
(0.125) 		0.705
(0.918) 		0.664
(0.902) 		0.219
(0.576) 		0.00023
(0.00876) 		0.679
(0.906) 		0.00702
(0.0824) 		0.0376
(0.211)
22q loss 201 (33%) 413 0.0523
(0.26) 		0.655
(0.898) 		0.696
(0.917) 		0.00209
(0.0339) 		0.374
(0.72) 		1e-05
(0.000888) 		0.00266
(0.0404) 		0.667
(0.903) 		0.841
(0.985) 		0.0202
(0.147) 		0.362
(0.707) 		0.000189
(0.00777) 		0.331
(0.685)
1q gain 113 (18%) 501 0.393
(0.742) 		0.742
(0.939) 		0.407
(0.748) 		0.303
(0.665) 		0.0294
(0.186) 		0.0258
(0.171) 		0.0492
(0.25) 		0.532
(0.834) 		0.14
(0.46) 		0.173
(0.504) 		0.757
(0.951) 		0.00198
(0.0339) 		1
(1.00)
3q gain 98 (16%) 516 0.169
(0.503) 		0.34
(0.69) 		0.0449
(0.235) 		0.0174
(0.142) 		0.796
(0.972) 		0.0434
(0.229) 		0.0305
(0.189) 		0.44
(0.783) 		0.801
(0.972) 		0.067
(0.295) 		0.615
(0.877) 		0.0677
(0.296) 		1
(1.00)
5p gain 106 (17%) 508 0.615
(0.877) 		0.102
(0.387) 		0.0394
(0.216) 		0.125
(0.435) 		0.828
(0.977) 		0.0248
(0.167) 		0.212
(0.566) 		0.915
(1.00) 		0.132
(0.447) 		0.0181
(0.144) 		0.28
(0.643) 		0.0182
(0.144) 		0.591
(0.863)
6q gain 111 (18%) 503 0.301
(0.662) 		0.613
(0.877) 		0.34
(0.69) 		0.0154
(0.131) 		0.762
(0.952) 		0.0021
(0.0339) 		0.0136
(0.124) 		0.529
(0.834) 		0.205
(0.554) 		0.145
(0.464) 		0.351
(0.694) 		0.00401
(0.0542) 		0.588
(0.862)
11p gain 85 (14%) 529 0.634
(0.889) 		0.00354
(0.0494) 		0.0239
(0.166) 		0.243
(0.607) 		0.146
(0.465) 		0.152
(0.476) 		0.0264
(0.174) 		1
(1.00) 		1
(1.00) 		0.00155
(0.0297) 		0.608
(0.877) 		0.128
(0.439) 		0.569
(0.852)
16p gain 148 (24%) 466 0.158
(0.49) 		0.181
(0.517) 		0.669
(0.903) 		0.0079
(0.0886) 		1
(1.00) 		0.00164
(0.0301) 		0.334
(0.687) 		1
(1.00) 		0.513
(0.825) 		0.00078
(0.0193) 		0.99
(1.00) 		0.00208
(0.0339) 		1
(1.00)
16q gain 145 (24%) 469 0.397
(0.745) 		0.139
(0.459) 		0.59
(0.862) 		0.00363
(0.0496) 		0.978
(1.00) 		0.00052
(0.0158) 		0.265
(0.629) 		0.924
(1.00) 		1
(1.00) 		0.00091
(0.0209) 		0.98
(1.00) 		0.00237
(0.0367) 		1
(1.00)
18p gain 31 (5%) 583 0.167
(0.503) 		0.798
(0.972) 		1
(1.00) 		0.0243
(0.166) 		0.734
(0.934) 		0.00832
(0.0914) 		1
(1.00) 		0.201
(0.549) 		0.149
(0.468) 		0.0328
(0.198) 		1
(1.00) 		0.0144
(0.128) 		1
(1.00)
1p loss 139 (23%) 475 0.0887
(0.35) 		0.445
(0.787) 		0.0812
(0.332) 		0.122
(0.433) 		0.891
(1.00) 		0.0172
(0.142) 		0.00841
(0.0915) 		0.246
(0.607) 		0.824
(0.977) 		0.011
(0.108) 		0.589
(0.862) 		0.00357
(0.0494) 		0.324
(0.681)
4q loss 189 (31%) 425 0.832
(0.977) 		0.688
(0.911) 		0.0126
(0.12) 		0.0762
(0.316) 		0.811
(0.974) 		0.0078
(0.0886) 		0.127
(0.439) 		0.54
(0.837) 		0.147
(0.468) 		0.00986
(0.103) 		0.902
(1.00) 		0.00608
(0.0753) 		0.173
(0.504)
5p loss 84 (14%) 530 0.554
(0.847) 		0.747
(0.94) 		0.506
(0.823) 		0.0373
(0.211) 		0.92
(1.00) 		0.0382
(0.212) 		0.312
(0.67) 		0.638
(0.889) 		1
(1.00) 		0.438
(0.781) 		0.345
(0.692) 		0.0358
(0.206) 		0.0249
(0.167)
10p loss 101 (16%) 513 0.127
(0.439) 		0.00327
(0.0471) 		0.137
(0.455) 		0.273
(0.638) 		0.783
(0.966) 		0.118
(0.43) 		0.21
(0.561) 		0.914
(1.00) 		0.00995
(0.103) 		0.0209
(0.15) 		0.92
(1.00) 		0.0233
(0.162) 		1
(1.00)
14q loss 205 (33%) 409 0.8
(0.972) 		0.278
(0.643) 		0.0199
(0.147) 		0.278
(0.643) 		0.431
(0.771) 		0.0379
(0.211) 		0.0489
(0.249) 		0.493
(0.818) 		0.315
(0.673) 		1e-05
(0.000888) 		0.992
(1.00) 		0.206
(0.555) 		0.664
(0.902)
15q loss 229 (37%) 385 0.411
(0.751) 		0.641
(0.889) 		0.0711
(0.304) 		0.0536
(0.264) 		0.35
(0.694) 		0.0192
(0.147) 		0.00819
(0.0909) 		0.277
(0.643) 		0.325
(0.681) 		0.00787
(0.0886) 		0.908
(1.00) 		0.00586
(0.0744) 		1
(1.00)
19p loss 62 (10%) 552 0.136
(0.455) 		0.119
(0.43) 		0.284
(0.646) 		0.00091
(0.0209) 		0.722
(0.923) 		0.00016
(0.00682) 		0.0101
(0.103) 		0.688
(0.911) 		1
(1.00) 		0.311
(0.67) 		0.52
(0.828) 		6.04e-06
(0.000888) 		1
(1.00)
2q gain 122 (20%) 492 0.495
(0.819) 		0.451
(0.788) 		0.03
(0.188) 		0.506
(0.823) 		0.443
(0.787) 		0.028
(0.18) 		0.456
(0.794) 		0.267
(0.629) 		0.158
(0.49) 		0.00642
(0.0769) 		0.266
(0.629) 		0.121
(0.432) 		0.33
(0.684)
8q gain 315 (51%) 299 0.133
(0.447) 		0.086
(0.342) 		0.522
(0.828) 		0.0331
(0.198) 		0.202
(0.55) 		0.0685
(0.296) 		0.0199
(0.147) 		0.747
(0.94) 		0.703
(0.918) 		0.0196
(0.147) 		0.119
(0.43) 		0.172
(0.504) 		1
(1.00)
9p gain 124 (20%) 490 0.0046
(0.0613) 		0.827
(0.977) 		0.0411
(0.221) 		0.0602
(0.28) 		0.542
(0.837) 		0.339
(0.69) 		0.558
(0.847) 		0.763
(0.952) 		0.813
(0.974) 		0.0131
(0.122) 		0.32
(0.679) 		0.366
(0.712) 		0.248
(0.608)
9q loss 77 (13%) 537 0.502
(0.823) 		0.0525
(0.26) 		0.578
(0.861) 		0.54
(0.837) 		0.119
(0.43) 		0.486
(0.813) 		0.0355
(0.206) 		0.465
(0.798) 		0.406
(0.748) 		0.0201
(0.147) 		0.104
(0.391) 		0.236
(0.601) 		0.02
(0.147)
10q loss 110 (18%) 504 0.109
(0.405) 		0.0085
(0.0915) 		0.0566
(0.271) 		0.495
(0.819) 		0.987
(1.00) 		0.293
(0.654) 		0.55
(0.845) 		0.916
(1.00) 		0.006
(0.0752) 		0.0152
(0.131) 		1
(1.00) 		0.123
(0.434) 		1
(1.00)
19q loss 56 (9%) 558 0.294
(0.654) 		0.676
(0.906) 		0.199
(0.548) 		0.0109
(0.108) 		0.762
(0.952) 		0.00161
(0.0301) 		0.0646
(0.29) 		0.328
(0.681) 		0.738
(0.935) 		0.27
(0.634) 		0.877
(1.00) 		0.000446
(0.0144) 		1
(1.00)
2p gain 123 (20%) 491 0.761
(0.952) 		0.806
(0.972) 		0.109
(0.405) 		0.564
(0.85) 		0.404
(0.748) 		0.0642
(0.29) 		0.301
(0.662) 		0.314
(0.673) 		0.345
(0.692) 		0.0179
(0.143) 		0.0416
(0.222) 		0.235
(0.601) 		0.342
(0.69)
3p gain 75 (12%) 539 0.922
(1.00) 		0.0852
(0.342) 		0.0243
(0.166) 		0.016
(0.136) 		1
(1.00) 		0.326
(0.681) 		0.142
(0.46) 		0.389
(0.735) 		1
(1.00) 		0.0743
(0.309) 		0.794
(0.972) 		0.155
(0.484) 		1
(1.00)
4q gain 21 (3%) 593 0.249
(0.608) 		0.797
(0.972) 		1
(1.00) 		0.379
(0.725) 		0.739
(0.936) 		0.0648
(0.29) 		0.0226
(0.159) 		0.267
(0.629) 		0.617
(0.877) 		0.416
(0.756) 		0.63
(0.889) 		0.043
(0.228) 		1
(1.00)
5q gain 65 (11%) 549 0.871
(1.00) 		0.811
(0.974) 		0.0258
(0.171) 		0.222
(0.58) 		0.806
(0.972) 		0.298
(0.66) 		0.568
(0.852) 		0.896
(1.00) 		0.112
(0.413) 		0.0356
(0.206) 		0.386
(0.73) 		0.451
(0.788) 		1
(1.00)
6p gain 122 (20%) 492 0.272
(0.638) 		0.434
(0.775) 		0.25
(0.608) 		0.0535
(0.264) 		0.588
(0.862) 		0.00057
(0.0169) 		0.0772
(0.319) 		0.311
(0.67) 		0.142
(0.46) 		0.31
(0.67) 		0.42
(0.757) 		0.00131
(0.0269) 		0.588
(0.862)
9q gain 103 (17%) 511 0.0132
(0.122) 		0.797
(0.972) 		0.179
(0.515) 		0.184
(0.522) 		0.638
(0.889) 		0.534
(0.835) 		0.636
(0.889) 		0.829
(0.977) 		0.795
(0.972) 		0.0366
(0.21) 		0.698
(0.918) 		0.625
(0.887) 		1
(1.00)
10p gain 49 (8%) 565 0.0399
(0.217) 		0.821
(0.977) 		0.613
(0.877) 		0.64
(0.889) 		0.217
(0.575) 		0.0457
(0.237) 		0.279
(0.643) 		1
(1.00) 		0.251
(0.61) 		0.821
(0.977) 		0.72
(0.923) 		0.218
(0.575) 		0.0734
(0.309)
11q gain 78 (13%) 536 0.19
(0.534) 		7.72e-05
(0.00449) 		0.169
(0.503) 		0.288
(0.649) 		0.467
(0.801) 		0.203
(0.552) 		0.0515
(0.259) 		1
(1.00) 		1
(1.00) 		0.0118
(0.115) 		0.722
(0.923) 		0.168
(0.503) 		0.532
(0.834)
12q gain 114 (19%) 500 0.652
(0.898) 		0.0617
(0.286) 		0.159
(0.49) 		0.116
(0.427) 		0.328
(0.681) 		0.0128
(0.121) 		0.37
(0.715) 		0.533
(0.834) 		1
(1.00) 		0.172
(0.504) 		0.565
(0.85) 		0.00558
(0.0725) 		0.592
(0.863)
18q gain 19 (3%) 595 0.777
(0.963) 		0.326
(0.681) 		0.603
(0.876) 		0.265
(0.629) 		0.443
(0.787) 		0.144
(0.462) 		1
(1.00) 		0.243
(0.607) 		0.0472
(0.243) 		0.0409
(0.221) 		0.868
(1.00) 		0.192
(0.538) 		1
(1.00)
1q loss 82 (13%) 532 0.188
(0.529) 		0.0951
(0.371) 		0.282
(0.645) 		0.397
(0.745) 		0.878
(1.00) 		0.409
(0.749) 		0.0164
(0.136) 		0.0438
(0.23) 		1
(1.00) 		0.195
(0.54) 		0.218
(0.575) 		0.25
(0.608) 		0.141
(0.46)
2p loss 17 (3%) 597 0.587
(0.862) 		0.206
(0.555) 		0.00092
(0.0209) 		0.541
(0.837) 		0.883
(1.00) 		0.796
(0.972) 		0.489
(0.816) 		0.806
(0.972) 		0.207
(0.555) 		0.00978
(0.103) 		1
(1.00) 		0.7
(0.918) 		1
(1.00)
3q loss 44 (7%) 570 0.245
(0.607) 		0.405
(0.748) 		0.475
(0.809) 		0.351
(0.694) 		0.131
(0.444) 		0.491
(0.817) 		0.0385
(0.212) 		0.16
(0.491) 		1
(1.00) 		0.00703
(0.0824) 		0.499
(0.823) 		0.513
(0.825) 		1
(1.00)
6p loss 46 (7%) 568 0.0176
(0.142) 		0.23
(0.593) 		1
(1.00) 		0.323
(0.681) 		0.633
(0.889) 		0.459
(0.797) 		0.828
(0.977) 		0.648
(0.894) 		0.0217
(0.154) 		0.18
(0.515) 		0.0791
(0.326) 		0.502
(0.823) 		1
(1.00)
6q loss 68 (11%) 546 0.0743
(0.309) 		0.763
(0.952) 		0.305
(0.665) 		0.638
(0.889) 		0.358
(0.704) 		0.0683
(0.296) 		0.347
(0.692) 		0.246
(0.607) 		0.0107
(0.108) 		0.0358
(0.206) 		0.174
(0.507) 		0.0501
(0.253) 		1
(1.00)
9p loss 75 (12%) 539 0.327
(0.681) 		0.286
(0.648) 		0.574
(0.857) 		0.643
(0.891) 		0.168
(0.503) 		0.385
(0.73) 		0.0572
(0.271) 		0.139
(0.457) 		1
(1.00) 		0.0212
(0.151) 		0.0136
(0.124) 		0.0737
(0.309) 		0.126
(0.438)
11p loss 74 (12%) 540 0.552
(0.847) 		0.501
(0.823) 		0.324
(0.681) 		0.148
(0.468) 		0.464
(0.798) 		0.0102
(0.103) 		0.363
(0.708) 		0.71
(0.918) 		0.135
(0.453) 		0.225
(0.583) 		0.897
(1.00) 		0.000373
(0.0128) 		1
(1.00)
12p loss 71 (12%) 543 0.0564
(0.271) 		0.414
(0.753) 		0.318
(0.677) 		0.255
(0.616) 		0.367
(0.712) 		0.056
(0.271) 		0.264
(0.629) 		0.53
(0.834) 		0.766
(0.955) 		0.0115
(0.113) 		0.881
(1.00) 		0.0289
(0.183) 		1
(1.00)
12q loss 71 (12%) 543 0.103
(0.388) 		0.901
(1.00) 		0.668
(0.903) 		0.0525
(0.26) 		0.589
(0.862) 		0.0301
(0.188) 		0.136
(0.455) 		0.9
(1.00) 		0.56
(0.847) 		0.0659
(0.292) 		1
(1.00) 		0.00642
(0.0769) 		1
(1.00)
13q loss 18 (3%) 596 0.244
(0.607) 		0.858
(0.997) 		0.588
(0.862) 		0.71
(0.918) 		0.657
(0.898) 		0.0856
(0.342) 		0.485
(0.813) 		0.815
(0.976) 		0.165
(0.503) 		0.0459
(0.237) 		1
(1.00) 		0.0283
(0.18) 		1
(1.00)
17q loss 93 (15%) 521 0.12
(0.43) 		0.743
(0.939) 		0.523
(0.828) 		0.1
(0.383) 		0.168
(0.503) 		0.014
(0.126) 		0.0936
(0.367) 		0.736
(0.934) 		1
(1.00) 		0.728
(0.928) 		0.463
(0.798) 		0.00155
(0.0297) 		1
(1.00)
xp loss 90 (15%) 524 0.187
(0.526) 		0.641
(0.889) 		0.52
(0.828) 		0.485
(0.813) 		0.465
(0.798) 		0.0324
(0.197) 		0.0742
(0.309) 		0.493
(0.818) 		0.593
(0.863) 		0.262
(0.629) 		0.952
(1.00) 		0.0176
(0.142) 		1
(1.00)
10q gain 29 (5%) 585 0.479
(0.812) 		0.12
(0.43) 		0.527
(0.832) 		0.735
(0.934) 		0.544
(0.839) 		0.137
(0.456) 		0.38
(0.725) 		1
(1.00) 		1
(1.00) 		0.86
(0.997) 		0.847
(0.989) 		0.0923
(0.363) 		0.0244
(0.166)
17p gain 39 (6%) 575 0.0279
(0.18) 		0.589
(0.862) 		1
(1.00) 		0.572
(0.856) 		0.316
(0.673) 		0.853
(0.993) 		0.627
(0.889) 		1
(1.00) 		0.711
(0.918) 		0.831
(0.977) 		1
(1.00) 		0.902
(1.00) 		0.306
(0.667)
17q gain 113 (18%) 501 0.085
(0.342) 		0.308
(0.67) 		0.814
(0.975) 		0.228
(0.589) 		0.694
(0.916) 		0.419
(0.757) 		0.031
(0.19) 		0.677
(0.906) 		0.808
(0.973) 		0.342
(0.69) 		0.179
(0.515) 		0.831
(0.977) 		0.0579
(0.271)
21q gain 34 (6%) 580 0.971
(1.00) 		0.0192
(0.147) 		0.685
(0.911) 		0.634
(0.889) 		0.196
(0.54) 		0.521
(0.828) 		0.42
(0.757) 		0.486
(0.813) 		0.66
(0.901) 		0.491
(0.817) 		0.839
(0.984) 		0.221
(0.58) 		1
(1.00)
7p loss 3 (0%) 611 0.476
(0.809) 		0.884
(1.00) 		1
(1.00) 		1
(1.00) 		0.682
(0.907) 		0.582
(0.862) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.124
(0.434) 		1
(1.00) 		0.148
(0.468) 		0.0279
(0.18)
7q loss 5 (1%) 609 0.33
(0.684) 		0.669
(0.903) 		0.613
(0.877) 		0.52
(0.828) 		0.417
(0.756) 		0.83
(0.977) 		1
(1.00) 		0.67
(0.903) 		0.254
(0.616) 		0.184
(0.522) 		1
(1.00) 		0.195
(0.54) 		0.0415
(0.222)
11q loss 91 (15%) 523 0.378
(0.724) 		0.554
(0.847) 		0.298
(0.66) 		0.377
(0.724) 		0.733
(0.934) 		0.0627
(0.288) 		0.246
(0.607) 		0.65
(0.896) 		0.183
(0.52) 		0.117
(0.429) 		0.922
(1.00) 		0.0398
(0.217) 		0.54
(0.837)
xq loss 78 (13%) 536 0.679
(0.906) 		0.981
(1.00) 		0.216
(0.574) 		0.483
(0.813) 		0.678
(0.906) 		0.235
(0.601) 		0.0164
(0.136) 		0.904
(1.00) 		0.769
(0.955) 		0.401
(0.747) 		0.4
(0.747) 		0.148
(0.468) 		1
(1.00)
1p gain 50 (8%) 564 0.453
(0.79) 		0.913
(1.00) 		0.613
(0.877) 		0.559
(0.847) 		0.558
(0.847) 		0.314
(0.673) 		0.279
(0.643) 		0.465
(0.798) 		0.723
(0.923) 		0.0563
(0.271) 		0.3
(0.662) 		0.068
(0.296) 		0.414
(0.753)
4p gain 20 (3%) 594 0.712
(0.918) 		0.384
(0.73) 		0.0711
(0.304) 		0.481
(0.812) 		0.338
(0.69) 		0.778
(0.963) 		0.31
(0.67) 		0.171
(0.504) 		1
(1.00) 		0.124
(0.434) 		0.688
(0.911) 		0.962
(1.00) 		1
(1.00)
8p gain 169 (28%) 445 0.781
(0.965) 		0.548
(0.844) 		0.26
(0.627) 		0.298
(0.66) 		0.617
(0.877) 		0.165
(0.503) 		0.514
(0.825) 		1
(1.00) 		0.83
(0.977) 		0.406
(0.748) 		0.074
(0.309) 		0.212
(0.566) 		1
(1.00)
12p gain 128 (21%) 486 0.336
(0.69) 		0.24
(0.607) 		0.91
(1.00) 		0.291
(0.654) 		0.294
(0.654) 		0.138
(0.457) 		0.665
(0.902) 		1
(1.00) 		0.144
(0.462) 		0.523
(0.828) 		0.794
(0.972) 		0.122
(0.433) 		0.588
(0.862)
14q gain 43 (7%) 571 0.462
(0.798) 		0.851
(0.991) 		0.283
(0.645) 		0.514
(0.825) 		0.955
(1.00) 		0.614
(0.877) 		0.358
(0.704) 		1
(1.00) 		1
(1.00) 		0.128
(0.439) 		0.29
(0.652) 		0.241
(0.607) 		1
(1.00)
15q gain 15 (2%) 599 0.76
(0.952) 		0.358
(0.704) 		1
(1.00) 		0.822
(0.977) 		0.0855
(0.342) 		0.721
(0.923) 		0.283
(0.645) 		0.0634
(0.29) 		0.508
(0.823) 		0.0829
(0.336) 		0.709
(0.918) 		0.411
(0.751) 		1
(1.00)
19p gain 105 (17%) 509 0.237
(0.602) 		0.913
(1.00) 		0.225
(0.583) 		0.855
(0.993) 		0.827
(0.977) 		0.341
(0.69) 		0.273
(0.638) 		0.283
(0.645) 		0.304
(0.665) 		0.0974
(0.378) 		0.384
(0.73) 		0.502
(0.823) 		0.588
(0.862)
19q gain 113 (18%) 501 0.199
(0.548) 		0.81
(0.974) 		0.638
(0.889) 		0.744
(0.939) 		0.956
(1.00) 		0.566
(0.852) 		0.285
(0.647) 		0.405
(0.748) 		1
(1.00) 		0.242
(0.607) 		0.175
(0.507) 		0.702
(0.918) 		0.277
(0.643)
22q gain 23 (4%) 591 0.992
(1.00) 		0.32
(0.679) 		0.0884
(0.35) 		0.675
(0.906) 		0.106
(0.395) 		0.278
(0.643) 		0.38
(0.725) 		0.833
(0.977) 		0.617
(0.877) 		0.1
(0.383) 		0.348
(0.692) 		0.109
(0.405) 		1
(1.00)
xp gain 100 (16%) 514 0.408
(0.748) 		0.778
(0.963) 		0.263
(0.629) 		0.129
(0.439) 		0.445
(0.787) 		0.124
(0.434) 		0.334
(0.687) 		0.1
(0.383) 		1
(1.00) 		0.156
(0.486) 		0.716
(0.922) 		0.682
(0.907) 		0.593
(0.863)
xq gain 109 (18%) 505 0.703
(0.918) 		0.475
(0.809) 		0.631
(0.889) 		0.1
(0.383) 		0.407
(0.748) 		0.17
(0.503) 		0.757
(0.951) 		0.17
(0.503) 		0.802
(0.972) 		0.701
(0.918) 		0.89
(1.00) 		0.245
(0.607) 		0.589
(0.862)
2q loss 14 (2%) 600 0.341
(0.69) 		0.503
(0.823) 		0.0624
(0.288) 		0.241
(0.607) 		1
(1.00) 		0.708
(0.918) 		0.141
(0.46) 		0.43
(0.77) 		0.508
(0.823) 		0.265
(0.629) 		0.847
(0.989) 		0.448
(0.788) 		1
(1.00)
8q loss 35 (6%) 579 0.803
(0.972) 		0.648
(0.894) 		0.554
(0.847) 		0.484
(0.813) 		0.907
(1.00) 		0.422
(0.759) 		0.194
(0.54) 		0.0799
(0.328) 		1
(1.00) 		0.657
(0.898) 		0.31
(0.67) 		0.56
(0.847) 		1
(1.00)
16p loss 40 (7%) 574 0.294
(0.654) 		0.36
(0.705) 		0.711
(0.918) 		0.262
(0.629) 		0.224
(0.583) 		0.535
(0.835) 		0.473
(0.809) 		0.515
(0.825) 		0.711
(0.918) 		0.503
(0.823) 		0.162
(0.497) 		0.616
(0.877) 		0.347
(0.692)
16q loss 43 (7%) 571 0.701
(0.918) 		0.18
(0.515) 		0.372
(0.717) 		0.644
(0.892) 		0.706
(0.918) 		0.183
(0.52) 		1
(1.00) 		0.875
(1.00) 		0.457
(0.795) 		0.722
(0.923) 		0.45
(0.788) 		0.465
(0.798) 		0.337
(0.69)
20p loss 64 (10%) 550 0.674
(0.905) 		0.609
(0.877) 		0.366
(0.712) 		0.539
(0.837) 		0.612
(0.877) 		0.556
(0.847) 		0.565
(0.85) 		0.692
(0.914) 		0.509
(0.824) 		0.511
(0.825) 		0.784
(0.966) 		0.817
(0.977) 		0.405
(0.748)
20q loss 8 (1%) 606 0.485
(0.813) 		0.801
(0.972) 		0.688
(0.911) 		0.241
(0.607) 		0.423
(0.759) 		0.888
(1.00) 		0.605
(0.877) 		1
(1.00) 		1
(1.00) 		0.789
(0.971) 		1
(1.00) 		0.827
(0.977) 		1
(1.00)
'1q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0294 (Fisher's exact test), Q value = 0.19

Table S1.  Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 20 105 417 69
1Q GAIN MUTATED 4 13 75 21
1Q GAIN WILD-TYPE 16 92 342 48

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

'1q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0258 (Fisher's exact test), Q value = 0.17

Table S2.  Gene #2: '1q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
1Q GAIN MUTATED 52 30 30
1Q GAIN WILD-TYPE 294 120 85

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'1q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0492 (Fisher's exact test), Q value = 0.25

Table S3.  Gene #2: '1q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
1Q GAIN MUTATED 76 23
1Q GAIN WILD-TYPE 377 65

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'1q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00198 (Wilcoxon-test), Q value = 0.034

Table S4.  Gene #2: '1q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
1Q GAIN MUTATED 108 3.5 (6.1)
1Q GAIN WILD-TYPE 472 1.9 (4.3)

Figure S4.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0179 (Fisher's exact test), Q value = 0.14

Table S5.  Gene #3: '2p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
2P GAIN MUTATED 75 8 40 0
2P GAIN WILD-TYPE 307 54 106 13

Figure S5.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'2p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0416 (Fisher's exact test), Q value = 0.22

Table S6.  Gene #3: '2p gain' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 446 6 37 29
2P GAIN MUTATED 86 3 5 10
2P GAIN WILD-TYPE 360 3 32 19

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

'2q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.03 (Fisher's exact test), Q value = 0.19

Table S7.  Gene #4: '2q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
2Q GAIN MUTATED 80 42
2Q GAIN WILD-TYPE 368 120

Figure S7.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'2q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.028 (Fisher's exact test), Q value = 0.18

Table S8.  Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
2Q GAIN MUTATED 59 29 33
2Q GAIN WILD-TYPE 287 121 82

Figure S8.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'2q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00642 (Fisher's exact test), Q value = 0.077

Table S9.  Gene #4: '2q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
2Q GAIN MUTATED 72 8 42 0
2Q GAIN WILD-TYPE 310 54 104 13

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0243 (Fisher's exact test), Q value = 0.17

Table S10.  Gene #5: '3p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
3P GAIN MUTATED 46 28
3P GAIN WILD-TYPE 402 134

Figure S10.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'3p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.016 (Fisher's exact test), Q value = 0.14

Table S11.  Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
3P GAIN MUTATED 9 1 2 21 1 0 5 4 6 7 9 4 2
3P GAIN WILD-TYPE 95 0 35 151 11 2 19 11 78 48 54 20 0

Figure S11.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'3q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0449 (Fisher's exact test), Q value = 0.23

Table S12.  Gene #6: '3q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
3Q GAIN MUTATED 63 34
3Q GAIN WILD-TYPE 385 128

Figure S12.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'3q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0174 (Fisher's exact test), Q value = 0.14

Table S13.  Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
3Q GAIN MUTATED 11 1 4 23 1 0 6 5 11 10 13 6 2
3Q GAIN WILD-TYPE 93 0 33 149 11 2 18 10 73 45 50 18 0

Figure S13.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'3q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0434 (Fisher's exact test), Q value = 0.23

Table S14.  Gene #6: '3q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
3Q GAIN MUTATED 44 31 22
3Q GAIN WILD-TYPE 302 119 93

Figure S14.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'3q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0305 (Fisher's exact test), Q value = 0.19

Table S15.  Gene #6: '3q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
3Q GAIN MUTATED 59 20
3Q GAIN WILD-TYPE 394 68

Figure S15.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'4q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0226 (Fisher's exact test), Q value = 0.16

Table S16.  Gene #8: '4q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
4Q GAIN MUTATED 12 7
4Q GAIN WILD-TYPE 441 81

Figure S16.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'4q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.043 (Wilcoxon-test), Q value = 0.23

Table S17.  Gene #8: '4q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
4Q GAIN MUTATED 21 2.3 (2.1)
4Q GAIN WILD-TYPE 559 2.2 (4.8)

Figure S17.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'5p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0394 (Fisher's exact test), Q value = 0.22

Table S18.  Gene #9: '5p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
5P GAIN MUTATED 69 37
5P GAIN WILD-TYPE 379 125

Figure S18.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'5p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0248 (Fisher's exact test), Q value = 0.17

Table S19.  Gene #9: '5p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
5P GAIN MUTATED 47 32 26
5P GAIN WILD-TYPE 299 118 89

Figure S19.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0181 (Fisher's exact test), Q value = 0.14

Table S20.  Gene #9: '5p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
5P GAIN MUTATED 61 8 37 0
5P GAIN WILD-TYPE 321 54 109 13

Figure S20.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0182 (Wilcoxon-test), Q value = 0.14

Table S21.  Gene #9: '5p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
5P GAIN MUTATED 103 2.7 (4.3)
5P GAIN WILD-TYPE 477 2.1 (4.8)

Figure S21.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'5q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0258 (Fisher's exact test), Q value = 0.17

Table S22.  Gene #10: '5q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
5Q GAIN MUTATED 40 25
5Q GAIN WILD-TYPE 408 137

Figure S22.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'5q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0356 (Fisher's exact test), Q value = 0.21

Table S23.  Gene #10: '5q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
5Q GAIN MUTATED 36 4 25 0
5Q GAIN WILD-TYPE 346 58 121 13

Figure S23.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'6p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00057 (Fisher's exact test), Q value = 0.017

Table S24.  Gene #11: '6p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
6P GAIN MUTATED 53 30 37
6P GAIN WILD-TYPE 293 120 78

Figure S24.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'6p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00131 (Wilcoxon-test), Q value = 0.027

Table S25.  Gene #11: '6p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
6P GAIN MUTATED 118 3.3 (5.2)
6P GAIN WILD-TYPE 462 2.0 (4.5)

Figure S25.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'6q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0154 (Fisher's exact test), Q value = 0.13

Table S26.  Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
6Q GAIN MUTATED 16 0 4 20 2 0 4 4 17 14 13 11 1
6Q GAIN WILD-TYPE 88 1 33 152 10 2 20 11 67 41 50 13 1

Figure S26.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0021 (Fisher's exact test), Q value = 0.034

Table S27.  Gene #12: '6q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
6Q GAIN MUTATED 48 28 33
6Q GAIN WILD-TYPE 298 122 82

Figure S27.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'6q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0136 (Fisher's exact test), Q value = 0.12

Table S28.  Gene #12: '6q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
6Q GAIN MUTATED 71 24
6Q GAIN WILD-TYPE 382 64

Figure S28.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'6q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00401 (Wilcoxon-test), Q value = 0.054

Table S29.  Gene #12: '6q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
6Q GAIN MUTATED 107 3.1 (4.8)
6Q GAIN WILD-TYPE 473 2.0 (4.7)

Figure S29.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'7p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0067

Table S30.  Gene #13: '7p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
7P GAIN MUTATED 57 1 19 72 3 1 13 11 60 37 42 16 1
7P GAIN WILD-TYPE 47 0 18 100 9 1 11 4 24 18 21 8 1

Figure S30.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'7p gain' versus 'PATHOLOGY_N_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00089

Table S31.  Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
7P GAIN MUTATED 167 103 75
7P GAIN WILD-TYPE 179 47 40

Figure S31.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0193 (Fisher's exact test), Q value = 0.15

Table S32.  Gene #13: '7p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
7P GAIN MUTATED 242 59
7P GAIN WILD-TYPE 211 29

Figure S32.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00026 (Fisher's exact test), Q value = 0.0096

Table S33.  Gene #13: '7p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
7P GAIN MUTATED 218 25 98 3
7P GAIN WILD-TYPE 164 37 48 10

Figure S33.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 7.06e-05 (Wilcoxon-test), Q value = 0.0044

Table S34.  Gene #13: '7p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
7P GAIN MUTATED 331 2.6 (5.2)
7P GAIN WILD-TYPE 249 1.7 (3.9)

Figure S34.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'7q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0053

Table S35.  Gene #14: '7q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
7Q GAIN MUTATED 54 1 17 61 3 1 12 7 56 32 38 16 1
7Q GAIN WILD-TYPE 50 0 20 111 9 1 12 8 28 23 25 8 1

Figure S35.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'7q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00072 (Fisher's exact test), Q value = 0.018

Table S36.  Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
7Q GAIN MUTATED 151 90 67
7Q GAIN WILD-TYPE 195 60 48

Figure S36.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'7q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00743 (Fisher's exact test), Q value = 0.086

Table S37.  Gene #14: '7q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
7Q GAIN MUTATED 212 55
7Q GAIN WILD-TYPE 241 33

Figure S37.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00326 (Fisher's exact test), Q value = 0.047

Table S38.  Gene #14: '7q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
7Q GAIN MUTATED 198 23 83 2
7Q GAIN WILD-TYPE 184 39 63 11

Figure S38.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00189 (Wilcoxon-test), Q value = 0.034

Table S39.  Gene #14: '7q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
7Q GAIN MUTATED 298 2.4 (4.7)
7Q GAIN WILD-TYPE 282 2.0 (4.7)

Figure S39.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'8q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0331 (Fisher's exact test), Q value = 0.2

Table S40.  Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
8Q GAIN MUTATED 45 0 21 84 3 2 10 10 42 33 42 13 0
8Q GAIN WILD-TYPE 59 1 16 88 9 0 14 5 42 22 21 11 2

Figure S40.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'8q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0199 (Fisher's exact test), Q value = 0.15

Table S41.  Gene #16: '8q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
8Q GAIN MUTATED 221 55
8Q GAIN WILD-TYPE 232 33

Figure S41.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'8q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0196 (Fisher's exact test), Q value = 0.15

Table S42.  Gene #16: '8q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
8Q GAIN MUTATED 203 22 81 4
8Q GAIN WILD-TYPE 179 40 65 9

Figure S42.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9p gain' versus 'Time to Death'

P value = 0.0046 (logrank test), Q value = 0.061

Table S43.  Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 594 128 0.0 - 148.0 (22.0)
9P GAIN MUTATED 120 36 0.0 - 129.3 (19.6)
9P GAIN WILD-TYPE 474 92 0.0 - 148.0 (23.3)

Figure S43.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0411 (Fisher's exact test), Q value = 0.22

Table S44.  Gene #17: '9p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
9P GAIN MUTATED 82 42
9P GAIN WILD-TYPE 366 120

Figure S44.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0131 (Fisher's exact test), Q value = 0.12

Table S45.  Gene #17: '9p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
9P GAIN MUTATED 64 18 36 5
9P GAIN WILD-TYPE 318 44 110 8

Figure S45.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9q gain' versus 'Time to Death'

P value = 0.0132 (logrank test), Q value = 0.12

Table S46.  Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 594 128 0.0 - 148.0 (22.0)
9Q GAIN MUTATED 100 30 0.0 - 129.3 (17.8)
9Q GAIN WILD-TYPE 494 98 0.0 - 148.0 (23.3)

Figure S46.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0366 (Fisher's exact test), Q value = 0.21

Table S47.  Gene #18: '9q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
9Q GAIN MUTATED 54 16 28 4
9Q GAIN WILD-TYPE 328 46 118 9

Figure S47.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'Time to Death'

P value = 0.0399 (logrank test), Q value = 0.22

Table S48.  Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 594 128 0.0 - 148.0 (22.0)
10P GAIN MUTATED 44 14 0.0 - 91.8 (20.8)
10P GAIN WILD-TYPE 550 114 0.0 - 148.0 (22.1)

Figure S48.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

'10p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0457 (Fisher's exact test), Q value = 0.24

Table S49.  Gene #19: '10p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
10P GAIN MUTATED 24 9 16
10P GAIN WILD-TYPE 322 141 99

Figure S49.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'10q gain' versus 'ETHNICITY'

P value = 0.0244 (Fisher's exact test), Q value = 0.17

Table S50.  Gene #20: '10q gain' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 352
10Q GAIN MUTATED 2 17
10Q GAIN WILD-TYPE 3 335

Figure S50.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #13: 'ETHNICITY'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00354 (Wilcoxon-test), Q value = 0.049

Table S51.  Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 612 66.3 (12.8)
11P GAIN MUTATED 85 62.6 (12.0)
11P GAIN WILD-TYPE 527 66.8 (12.8)

Figure S51.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0239 (Fisher's exact test), Q value = 0.17

Table S52.  Gene #21: '11p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
11P GAIN MUTATED 53 31
11P GAIN WILD-TYPE 395 131

Figure S52.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0264 (Fisher's exact test), Q value = 0.17

Table S53.  Gene #21: '11p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
11P GAIN MUTATED 55 19
11P GAIN WILD-TYPE 398 69

Figure S53.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00155 (Fisher's exact test), Q value = 0.03

Table S54.  Gene #21: '11p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
11P GAIN MUTATED 51 2 31 0
11P GAIN WILD-TYPE 331 60 115 13

Figure S54.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 7.72e-05 (Wilcoxon-test), Q value = 0.0045

Table S55.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 612 66.3 (12.8)
11Q GAIN MUTATED 78 61.0 (12.2)
11Q GAIN WILD-TYPE 534 67.0 (12.7)

Figure S55.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0118 (Fisher's exact test), Q value = 0.11

Table S56.  Gene #22: '11q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
11Q GAIN MUTATED 50 2 26 0
11Q GAIN WILD-TYPE 332 60 120 13

Figure S56.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0128 (Fisher's exact test), Q value = 0.12

Table S57.  Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
12Q GAIN MUTATED 77 25 12
12Q GAIN WILD-TYPE 269 125 103

Figure S57.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00558 (Wilcoxon-test), Q value = 0.073

Table S58.  Gene #24: '12q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
12Q GAIN MUTATED 110 1.1 (2.0)
12Q GAIN WILD-TYPE 470 2.5 (5.1)

Figure S58.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'13q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0147 (Fisher's exact test), Q value = 0.13

Table S59.  Gene #25: '13q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
13Q GAIN MUTATED 257 111
13Q GAIN WILD-TYPE 191 51

Figure S59.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'13q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00072 (Fisher's exact test), Q value = 0.018

Table S60.  Gene #25: '13q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
13Q GAIN MUTATED 62 0 19 85 5 2 14 13 55 38 48 17 0
13Q GAIN WILD-TYPE 42 1 18 87 7 0 10 2 29 17 15 7 2

Figure S60.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'13q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0053

Table S61.  Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
13Q GAIN MUTATED 184 104 81
13Q GAIN WILD-TYPE 162 46 34

Figure S61.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'13q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0121 (Fisher's exact test), Q value = 0.12

Table S62.  Gene #25: '13q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
13Q GAIN MUTATED 264 64
13Q GAIN WILD-TYPE 189 24

Figure S62.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00089

Table S63.  Gene #25: '13q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
13Q GAIN MUTATED 239 17 107 3
13Q GAIN WILD-TYPE 143 45 39 10

Figure S63.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'13q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000647 (Wilcoxon-test), Q value = 0.018

Table S64.  Gene #25: '13q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
13Q GAIN MUTATED 359 2.4 (4.1)
13Q GAIN WILD-TYPE 221 2.0 (5.5)

Figure S64.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'16p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0079 (Fisher's exact test), Q value = 0.089

Table S65.  Gene #28: '16p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
16P GAIN MUTATED 18 1 4 31 3 0 8 7 24 20 17 6 1
16P GAIN WILD-TYPE 86 0 33 141 9 2 16 8 60 35 46 18 1

Figure S65.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'16p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00164 (Fisher's exact test), Q value = 0.03

Table S66.  Gene #28: '16p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
16P GAIN MUTATED 64 46 36
16P GAIN WILD-TYPE 282 104 79

Figure S66.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00078 (Fisher's exact test), Q value = 0.019

Table S67.  Gene #28: '16p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
16P GAIN MUTATED 100 5 41 0
16P GAIN WILD-TYPE 282 57 105 13

Figure S67.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00208 (Wilcoxon-test), Q value = 0.034

Table S68.  Gene #28: '16p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
16P GAIN MUTATED 140 2.7 (4.4)
16P GAIN WILD-TYPE 440 2.1 (4.8)

Figure S68.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'16q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00363 (Fisher's exact test), Q value = 0.05

Table S69.  Gene #29: '16q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
16Q GAIN MUTATED 17 1 4 30 2 0 8 8 26 17 16 7 1
16Q GAIN WILD-TYPE 87 0 33 142 10 2 16 7 58 38 47 17 1

Figure S69.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'16q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00052 (Fisher's exact test), Q value = 0.016

Table S70.  Gene #29: '16q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
16Q GAIN MUTATED 61 48 34
16Q GAIN WILD-TYPE 285 102 81

Figure S70.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00091 (Fisher's exact test), Q value = 0.021

Table S71.  Gene #29: '16q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
16Q GAIN MUTATED 97 5 41 0
16Q GAIN WILD-TYPE 285 57 105 13

Figure S71.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00237 (Wilcoxon-test), Q value = 0.037

Table S72.  Gene #29: '16q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
16Q GAIN MUTATED 138 2.5 (3.8)
16Q GAIN WILD-TYPE 442 2.1 (5.0)

Figure S72.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'17p gain' versus 'Time to Death'

P value = 0.0279 (logrank test), Q value = 0.18

Table S73.  Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 594 128 0.0 - 148.0 (22.0)
17P GAIN MUTATED 39 2 1.0 - 148.0 (20.0)
17P GAIN WILD-TYPE 555 126 0.0 - 140.4 (22.0)

Figure S73.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

'17q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.031 (Fisher's exact test), Q value = 0.19

Table S74.  Gene #31: '17q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
17Q GAIN MUTATED 72 23
17Q GAIN WILD-TYPE 381 65

Figure S74.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'18p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0243 (Fisher's exact test), Q value = 0.17

Table S75.  Gene #32: '18p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
18P GAIN MUTATED 4 0 5 4 0 0 2 0 4 7 4 0 1
18P GAIN WILD-TYPE 100 1 32 168 12 2 22 15 80 48 59 24 1

Figure S75.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'18p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00832 (Fisher's exact test), Q value = 0.091

Table S76.  Gene #32: '18p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
18P GAIN MUTATED 13 5 13
18P GAIN WILD-TYPE 333 145 102

Figure S76.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0328 (Fisher's exact test), Q value = 0.2

Table S77.  Gene #32: '18p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
18P GAIN MUTATED 16 7 6 2
18P GAIN WILD-TYPE 366 55 140 11

Figure S77.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0144 (Wilcoxon-test), Q value = 0.13

Table S78.  Gene #32: '18p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
18P GAIN MUTATED 30 4.7 (6.9)
18P GAIN WILD-TYPE 550 2.1 (4.5)

Figure S78.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'18q gain' versus 'RADIATION_THERAPY'

P value = 0.0472 (Fisher's exact test), Q value = 0.24

Table S79.  Gene #33: '18q gain' versus Clinical Feature #9: 'RADIATION_THERAPY'

nPatients NO YES
ALL 482 29
18Q GAIN MUTATED 12 3
18Q GAIN WILD-TYPE 470 26

Figure S79.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #9: 'RADIATION_THERAPY'

'18q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0409 (Fisher's exact test), Q value = 0.22

Table S80.  Gene #33: '18q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
18Q GAIN MUTATED 8 5 5 1
18Q GAIN WILD-TYPE 374 57 141 12

Figure S80.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.00545 (Fisher's exact test), Q value = 0.072

Table S81.  Gene #36: '20p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
20P GAIN MUTATED 242 108
20P GAIN WILD-TYPE 206 54

Figure S81.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00096 (Fisher's exact test), Q value = 0.021

Table S82.  Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
20P GAIN MUTATED 63 1 14 86 4 1 12 13 46 32 48 16 1
20P GAIN WILD-TYPE 41 0 23 86 8 1 12 2 38 23 15 8 1

Figure S82.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'20p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0222 (Fisher's exact test), Q value = 0.16

Table S83.  Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
20P GAIN MUTATED 181 94 74
20P GAIN WILD-TYPE 165 56 41

Figure S83.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'20p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.000901 (Fisher's exact test), Q value = 0.021

Table S84.  Gene #36: '20p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
20P GAIN MUTATED 248 65
20P GAIN WILD-TYPE 205 23

Figure S84.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S85.  Gene #36: '20p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
20P GAIN MUTATED 219 20 101 5
20P GAIN WILD-TYPE 163 42 45 8

Figure S85.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0199 (Wilcoxon-test), Q value = 0.15

Table S86.  Gene #36: '20p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
20P GAIN MUTATED 338 2.4 (4.7)
20P GAIN WILD-TYPE 242 2.0 (4.6)

Figure S86.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'20q gain' versus 'TUMOR_TISSUE_SITE'

P value = 2.56e-06 (Fisher's exact test), Q value = 0.00089

Table S87.  Gene #37: '20q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
20Q GAIN MUTATED 315 143
20Q GAIN WILD-TYPE 133 19

Figure S87.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'20q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00036 (Fisher's exact test), Q value = 0.013

Table S88.  Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
20Q GAIN MUTATED 79 1 21 117 5 2 17 14 66 44 56 22 1
20Q GAIN WILD-TYPE 25 0 16 55 7 0 7 1 18 11 7 2 1

Figure S88.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 6e-04 (Fisher's exact test), Q value = 0.017

Table S89.  Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
20Q GAIN MUTATED 240 127 91
20Q GAIN WILD-TYPE 106 23 24

Figure S89.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'20q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00111 (Fisher's exact test), Q value = 0.023

Table S90.  Gene #37: '20q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
20Q GAIN MUTATED 330 78
20Q GAIN WILD-TYPE 123 10

Figure S90.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00089

Table S91.  Gene #37: '20q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
20Q GAIN MUTATED 287 25 134 7
20Q GAIN WILD-TYPE 95 37 12 6

Figure S91.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0349 (Fisher's exact test), Q value = 0.21

Table S92.  Gene #37: '20q gain' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 446 6 37 29
20Q GAIN MUTATED 333 5 32 16
20Q GAIN WILD-TYPE 113 1 5 13

Figure S92.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

'20q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00345 (Wilcoxon-test), Q value = 0.049

Table S93.  Gene #37: '20q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
20Q GAIN MUTATED 439 2.3 (4.7)
20Q GAIN WILD-TYPE 141 1.8 (4.7)

Figure S93.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0192 (Wilcoxon-test), Q value = 0.15

Table S94.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 612 66.3 (12.8)
21Q GAIN MUTATED 34 61.9 (11.3)
21Q GAIN WILD-TYPE 578 66.5 (12.8)

Figure S94.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0172 (Fisher's exact test), Q value = 0.14

Table S95.  Gene #42: '1p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
1P LOSS MUTATED 65 37 36
1P LOSS WILD-TYPE 281 113 79

Figure S95.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'1p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00841 (Fisher's exact test), Q value = 0.091

Table S96.  Gene #42: '1p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
1P LOSS MUTATED 94 30
1P LOSS WILD-TYPE 359 58

Figure S96.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'1p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.011 (Fisher's exact test), Q value = 0.11

Table S97.  Gene #42: '1p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
1P LOSS MUTATED 85 9 44 0
1P LOSS WILD-TYPE 297 53 102 13

Figure S97.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00357 (Wilcoxon-test), Q value = 0.049

Table S98.  Gene #42: '1p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
1P LOSS MUTATED 130 3.4 (6.3)
1P LOSS WILD-TYPE 450 1.9 (4.1)

Figure S98.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'1q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0164 (Fisher's exact test), Q value = 0.14

Table S99.  Gene #43: '1q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
1Q LOSS MUTATED 53 19
1Q LOSS WILD-TYPE 400 69

Figure S99.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'1q loss' versus 'GENDER'

P value = 0.0438 (Fisher's exact test), Q value = 0.23

Table S100.  Gene #43: '1q loss' versus Clinical Feature #8: 'GENDER'

nPatients FEMALE MALE
ALL 289 325
1Q LOSS MUTATED 30 52
1Q LOSS WILD-TYPE 259 273

Figure S100.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #8: 'GENDER'

'2p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00092 (Fisher's exact test), Q value = 0.021

Table S101.  Gene #44: '2p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
2P LOSS MUTATED 6 11
2P LOSS WILD-TYPE 442 151

Figure S101.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'2p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00978 (Fisher's exact test), Q value = 0.1

Table S102.  Gene #44: '2p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
2P LOSS MUTATED 6 0 9 1
2P LOSS WILD-TYPE 376 62 137 12

Figure S102.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'Time to Death'

P value = 0.031 (logrank test), Q value = 0.19

Table S103.  Gene #46: '3p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 594 128 0.0 - 148.0 (22.0)
3P LOSS MUTATED 66 16 0.2 - 85.0 (15.5)
3P LOSS WILD-TYPE 528 112 0.0 - 148.0 (23.3)

Figure S103.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0488 (Fisher's exact test), Q value = 0.25

Table S104.  Gene #46: '3p loss' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 20 105 417 69
3P LOSS MUTATED 2 4 51 9
3P LOSS WILD-TYPE 18 101 366 60

Figure S104.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0194 (Fisher's exact test), Q value = 0.15

Table S105.  Gene #46: '3p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
3P LOSS MUTATED 27 21 18
3P LOSS WILD-TYPE 319 129 97

Figure S105.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'3p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00101 (Fisher's exact test), Q value = 0.022

Table S106.  Gene #46: '3p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
3P LOSS MUTATED 39 19
3P LOSS WILD-TYPE 414 69

Figure S106.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'3p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0353 (Fisher's exact test), Q value = 0.21

Table S107.  Gene #46: '3p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
3P LOSS MUTATED 49 4 9 3
3P LOSS WILD-TYPE 333 58 137 10

Figure S107.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0146 (Wilcoxon-test), Q value = 0.13

Table S108.  Gene #46: '3p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
3P LOSS MUTATED 61 3.4 (5.6)
3P LOSS WILD-TYPE 519 2.1 (4.6)

Figure S108.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'3q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0385 (Fisher's exact test), Q value = 0.21

Table S109.  Gene #47: '3q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
3Q LOSS MUTATED 27 11
3Q LOSS WILD-TYPE 426 77

Figure S109.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'3q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00703 (Fisher's exact test), Q value = 0.082

Table S110.  Gene #47: '3q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
3Q LOSS MUTATED 31 3 5 4
3Q LOSS WILD-TYPE 351 59 141 9

Figure S110.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00638 (Fisher's exact test), Q value = 0.077

Table S111.  Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
4P LOSS MUTATED 26 0 6 50 3 0 6 8 25 23 31 11 1
4P LOSS WILD-TYPE 78 1 31 122 9 2 18 7 59 32 32 13 1

Figure S111.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00183 (Fisher's exact test), Q value = 0.033

Table S112.  Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
4P LOSS MUTATED 90 56 48
4P LOSS WILD-TYPE 256 94 67

Figure S112.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000626 (Fisher's exact test), Q value = 0.018

Table S113.  Gene #48: '4p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
4P LOSS MUTATED 128 42
4P LOSS WILD-TYPE 325 46

Figure S113.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0187 (Fisher's exact test), Q value = 0.15

Table S114.  Gene #48: '4p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
4P LOSS MUTATED 125 10 54 3
4P LOSS WILD-TYPE 257 52 92 10

Figure S114.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000718 (Wilcoxon-test), Q value = 0.018

Table S115.  Gene #48: '4p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
4P LOSS MUTATED 185 3.0 (5.1)
4P LOSS WILD-TYPE 395 1.8 (4.5)

Figure S115.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'4q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0126 (Fisher's exact test), Q value = 0.12

Table S116.  Gene #49: '4q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
4Q LOSS MUTATED 123 62
4Q LOSS WILD-TYPE 325 100

Figure S116.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0078 (Fisher's exact test), Q value = 0.089

Table S117.  Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
4Q LOSS MUTATED 89 55 44
4Q LOSS WILD-TYPE 257 95 71

Figure S117.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00986 (Fisher's exact test), Q value = 0.1

Table S118.  Gene #49: '4q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
4Q LOSS MUTATED 112 11 58 3
4Q LOSS WILD-TYPE 270 51 88 10

Figure S118.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00608 (Wilcoxon-test), Q value = 0.075

Table S119.  Gene #49: '4q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
4Q LOSS MUTATED 179 2.9 (5.1)
4Q LOSS WILD-TYPE 401 1.9 (4.5)

Figure S119.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0373 (Fisher's exact test), Q value = 0.21

Table S120.  Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
5P LOSS MUTATED 13 0 4 15 0 1 3 5 13 12 8 7 0
5P LOSS WILD-TYPE 91 1 33 157 12 1 21 10 71 43 55 17 2

Figure S120.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'5p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0382 (Fisher's exact test), Q value = 0.21

Table S121.  Gene #50: '5p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
5P LOSS MUTATED 37 27 20
5P LOSS WILD-TYPE 309 123 95

Figure S121.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'5p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0358 (Wilcoxon-test), Q value = 0.21

Table S122.  Gene #50: '5p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
5P LOSS MUTATED 81 3.6 (7.1)
5P LOSS WILD-TYPE 499 2.0 (4.1)

Figure S122.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'5p loss' versus 'ETHNICITY'

P value = 0.0249 (Fisher's exact test), Q value = 0.17

Table S123.  Gene #50: '5p loss' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 352
5P LOSS MUTATED 3 50
5P LOSS WILD-TYPE 2 302

Figure S123.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #13: 'ETHNICITY'

'5q loss' versus 'Time to Death'

P value = 0.0344 (logrank test), Q value = 0.2

Table S124.  Gene #51: '5q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 594 128 0.0 - 148.0 (22.0)
5Q LOSS MUTATED 115 33 0.2 - 126.4 (23.0)
5Q LOSS WILD-TYPE 479 95 0.0 - 148.0 (22.0)

Figure S124.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #1: 'Time to Death'

'5q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0372 (Fisher's exact test), Q value = 0.21

Table S125.  Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
5Q LOSS MUTATED 17 0 7 27 0 0 3 5 16 18 14 10 0
5Q LOSS WILD-TYPE 87 1 30 145 12 2 21 10 68 37 49 14 2

Figure S125.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0147 (Fisher's exact test), Q value = 0.13

Table S126.  Gene #51: '5q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
5Q LOSS MUTATED 56 31 33
5Q LOSS WILD-TYPE 290 119 82

Figure S126.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0377 (Fisher's exact test), Q value = 0.21

Table S127.  Gene #51: '5q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
5Q LOSS MUTATED 79 24
5Q LOSS WILD-TYPE 374 64

Figure S127.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'5q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0058 (Wilcoxon-test), Q value = 0.074

Table S128.  Gene #51: '5q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
5Q LOSS MUTATED 115 3.2 (5.6)
5Q LOSS WILD-TYPE 465 2.0 (4.4)

Figure S128.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'6p loss' versus 'Time to Death'

P value = 0.0176 (logrank test), Q value = 0.14

Table S129.  Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 594 128 0.0 - 148.0 (22.0)
6P LOSS MUTATED 45 13 2.0 - 45.4 (17.8)
6P LOSS WILD-TYPE 549 115 0.0 - 148.0 (22.4)

Figure S129.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'RADIATION_THERAPY'

P value = 0.0217 (Fisher's exact test), Q value = 0.15

Table S130.  Gene #52: '6p loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

nPatients NO YES
ALL 482 29
6P LOSS MUTATED 35 6
6P LOSS WILD-TYPE 447 23

Figure S130.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.0107 (Fisher's exact test), Q value = 0.11

Table S131.  Gene #53: '6q loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

nPatients NO YES
ALL 482 29
6Q LOSS MUTATED 50 8
6Q LOSS WILD-TYPE 432 21

Figure S131.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0358 (Fisher's exact test), Q value = 0.21

Table S132.  Gene #53: '6q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
6Q LOSS MUTATED 37 7 16 5
6Q LOSS WILD-TYPE 345 55 130 8

Figure S132.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'7p loss' versus 'ETHNICITY'

P value = 0.0279 (Fisher's exact test), Q value = 0.18

Table S133.  Gene #54: '7p loss' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 352
7P LOSS MUTATED 1 1
7P LOSS WILD-TYPE 4 351

Figure S133.  Get High-res Image Gene #54: '7p loss' versus Clinical Feature #13: 'ETHNICITY'

'7q loss' versus 'ETHNICITY'

P value = 0.0415 (Fisher's exact test), Q value = 0.22

Table S134.  Gene #55: '7q loss' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 352
7Q LOSS MUTATED 1 2
7Q LOSS WILD-TYPE 4 350

Figure S134.  Get High-res Image Gene #55: '7q loss' versus Clinical Feature #13: 'ETHNICITY'

'8p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00204 (Fisher's exact test), Q value = 0.034

Table S135.  Gene #56: '8p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
8P LOSS MUTATED 140 73
8P LOSS WILD-TYPE 308 89

Figure S135.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'8p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00912 (Fisher's exact test), Q value = 0.097

Table S136.  Gene #56: '8p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
8P LOSS MUTATED 30 0 9 49 2 0 10 8 30 25 33 11 1
8P LOSS WILD-TYPE 74 1 28 123 10 2 14 7 54 30 30 13 1

Figure S136.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'8p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.006

Table S137.  Gene #56: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
8P LOSS MUTATED 98 62 55
8P LOSS WILD-TYPE 248 88 60

Figure S137.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'8p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00232 (Fisher's exact test), Q value = 0.036

Table S138.  Gene #56: '8p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
8P LOSS MUTATED 148 44
8P LOSS WILD-TYPE 305 44

Figure S138.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00143 (Fisher's exact test), Q value = 0.029

Table S139.  Gene #56: '8p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
8P LOSS MUTATED 126 12 67 5
8P LOSS WILD-TYPE 256 50 79 8

Figure S139.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 1.86e-05 (Wilcoxon-test), Q value = 0.0014

Table S140.  Gene #56: '8p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
8P LOSS MUTATED 206 3.3 (6.2)
8P LOSS WILD-TYPE 374 1.6 (3.5)

Figure S140.  Get High-res Image Gene #56: '8p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0212 (Fisher's exact test), Q value = 0.15

Table S141.  Gene #58: '9p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
9P LOSS MUTATED 50 1 21 1
9P LOSS WILD-TYPE 332 61 125 12

Figure S141.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'RESIDUAL_TUMOR'

P value = 0.0136 (Fisher's exact test), Q value = 0.12

Table S142.  Gene #58: '9p loss' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 446 6 37 29
9P LOSS MUTATED 48 3 8 3
9P LOSS WILD-TYPE 398 3 29 26

Figure S142.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #11: 'RESIDUAL_TUMOR'

'9q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0355 (Fisher's exact test), Q value = 0.21

Table S143.  Gene #59: '9q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
9Q LOSS MUTATED 52 18
9Q LOSS WILD-TYPE 401 70

Figure S143.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0201 (Fisher's exact test), Q value = 0.15

Table S144.  Gene #59: '9q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
9Q LOSS MUTATED 51 1 21 1
9Q LOSS WILD-TYPE 331 61 125 12

Figure S144.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'ETHNICITY'

P value = 0.02 (Fisher's exact test), Q value = 0.15

Table S145.  Gene #59: '9q loss' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 352
9Q LOSS MUTATED 3 46
9Q LOSS WILD-TYPE 2 306

Figure S145.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #13: 'ETHNICITY'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00327 (Wilcoxon-test), Q value = 0.047

Table S146.  Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 612 66.3 (12.8)
10P LOSS MUTATED 101 62.7 (13.3)
10P LOSS WILD-TYPE 511 67.0 (12.6)

Figure S146.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'RADIATION_THERAPY'

P value = 0.00995 (Fisher's exact test), Q value = 0.1

Table S147.  Gene #60: '10p loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

nPatients NO YES
ALL 482 29
10P LOSS MUTATED 81 11
10P LOSS WILD-TYPE 401 18

Figure S147.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0209 (Fisher's exact test), Q value = 0.15

Table S148.  Gene #60: '10p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
10P LOSS MUTATED 61 6 27 6
10P LOSS WILD-TYPE 321 56 119 7

Figure S148.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0233 (Wilcoxon-test), Q value = 0.16

Table S149.  Gene #60: '10p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
10P LOSS MUTATED 96 2.7 (4.5)
10P LOSS WILD-TYPE 484 2.1 (4.7)

Figure S149.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0085 (Wilcoxon-test), Q value = 0.091

Table S150.  Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 612 66.3 (12.8)
10Q LOSS MUTATED 110 63.3 (12.7)
10Q LOSS WILD-TYPE 502 66.9 (12.7)

Figure S150.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'RADIATION_THERAPY'

P value = 0.006 (Fisher's exact test), Q value = 0.075

Table S151.  Gene #61: '10q loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

nPatients NO YES
ALL 482 29
10Q LOSS MUTATED 88 12
10Q LOSS WILD-TYPE 394 17

Figure S151.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #9: 'RADIATION_THERAPY'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0152 (Fisher's exact test), Q value = 0.13

Table S152.  Gene #61: '10q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
10Q LOSS MUTATED 66 6 31 6
10Q LOSS WILD-TYPE 316 56 115 7

Figure S152.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'11p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0102 (Fisher's exact test), Q value = 0.1

Table S153.  Gene #62: '11p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
11P LOSS MUTATED 30 24 20
11P LOSS WILD-TYPE 316 126 95

Figure S153.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'11p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000373 (Wilcoxon-test), Q value = 0.013

Table S154.  Gene #62: '11p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
11P LOSS MUTATED 70 3.8 (6.0)
11P LOSS WILD-TYPE 510 2.0 (4.4)

Figure S154.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'11q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0398 (Wilcoxon-test), Q value = 0.22

Table S155.  Gene #63: '11q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
11Q LOSS MUTATED 87 2.9 (5.5)
11Q LOSS WILD-TYPE 493 2.1 (4.5)

Figure S155.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0115 (Fisher's exact test), Q value = 0.11

Table S156.  Gene #64: '12p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
12P LOSS MUTATED 47 1 22 0
12P LOSS WILD-TYPE 335 61 124 13

Figure S156.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'12p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0289 (Wilcoxon-test), Q value = 0.18

Table S157.  Gene #64: '12p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
12P LOSS MUTATED 69 2.5 (4.0)
12P LOSS WILD-TYPE 511 2.2 (4.8)

Figure S157.  Get High-res Image Gene #64: '12p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'12q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0301 (Fisher's exact test), Q value = 0.19

Table S158.  Gene #65: '12q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
12Q LOSS MUTATED 30 22 19
12Q LOSS WILD-TYPE 316 128 96

Figure S158.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'12q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00642 (Wilcoxon-test), Q value = 0.077

Table S159.  Gene #65: '12q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
12Q LOSS MUTATED 68 3.0 (5.0)
12Q LOSS WILD-TYPE 512 2.1 (4.7)

Figure S159.  Get High-res Image Gene #65: '12q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0459 (Fisher's exact test), Q value = 0.24

Table S160.  Gene #66: '13q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
13Q LOSS MUTATED 8 3 4 2
13Q LOSS WILD-TYPE 374 59 142 11

Figure S160.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'13q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0283 (Wilcoxon-test), Q value = 0.18

Table S161.  Gene #66: '13q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
13Q LOSS MUTATED 15 8.8 (14.2)
13Q LOSS WILD-TYPE 565 2.0 (4.1)

Figure S161.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'14q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0199 (Fisher's exact test), Q value = 0.15

Table S162.  Gene #67: '14q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
14Q LOSS MUTATED 137 66
14Q LOSS WILD-TYPE 311 96

Figure S162.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'14q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0379 (Fisher's exact test), Q value = 0.21

Table S163.  Gene #67: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
14Q LOSS MUTATED 105 63 36
14Q LOSS WILD-TYPE 241 87 79

Figure S163.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'14q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0489 (Fisher's exact test), Q value = 0.25

Table S164.  Gene #67: '14q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
14Q LOSS MUTATED 145 38
14Q LOSS WILD-TYPE 308 50

Figure S164.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00089

Table S165.  Gene #67: '14q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
14Q LOSS MUTATED 131 3 64 1
14Q LOSS WILD-TYPE 251 59 82 12

Figure S165.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0192 (Fisher's exact test), Q value = 0.15

Table S166.  Gene #68: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
15Q LOSS MUTATED 113 66 50
15Q LOSS WILD-TYPE 233 84 65

Figure S166.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00819 (Fisher's exact test), Q value = 0.091

Table S167.  Gene #68: '15q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
15Q LOSS MUTATED 158 44
15Q LOSS WILD-TYPE 295 44

Figure S167.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00787 (Fisher's exact test), Q value = 0.089

Table S168.  Gene #68: '15q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
15Q LOSS MUTATED 142 12 64 5
15Q LOSS WILD-TYPE 240 50 82 8

Figure S168.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00586 (Wilcoxon-test), Q value = 0.074

Table S169.  Gene #68: '15q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
15Q LOSS MUTATED 215 2.7 (4.9)
15Q LOSS WILD-TYPE 365 1.9 (4.5)

Figure S169.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'17p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.027 (Fisher's exact test), Q value = 0.18

Table S170.  Gene #71: '17p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
17P LOSS MUTATED 233 101
17P LOSS WILD-TYPE 215 61

Figure S170.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'17p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00208 (Fisher's exact test), Q value = 0.034

Table S171.  Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
17P LOSS MUTATED 45 0 19 84 4 2 12 12 47 37 44 16 2
17P LOSS WILD-TYPE 59 1 18 88 8 0 12 3 37 18 19 8 0

Figure S171.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00109 (Fisher's exact test), Q value = 0.023

Table S172.  Gene #71: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
17P LOSS MUTATED 168 94 74
17P LOSS WILD-TYPE 178 56 41

Figure S172.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00221 (Fisher's exact test), Q value = 0.035

Table S173.  Gene #71: '17p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
17P LOSS MUTATED 238 62
17P LOSS WILD-TYPE 215 26

Figure S173.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00089

Table S174.  Gene #71: '17p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
17P LOSS MUTATED 216 14 94 6
17P LOSS WILD-TYPE 166 48 52 7

Figure S174.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00047 (Wilcoxon-test), Q value = 0.015

Table S175.  Gene #71: '17p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
17P LOSS MUTATED 319 2.7 (5.3)
17P LOSS WILD-TYPE 261 1.7 (3.8)

Figure S175.  Get High-res Image Gene #71: '17p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'17q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.014 (Fisher's exact test), Q value = 0.13

Table S176.  Gene #72: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
17Q LOSS MUTATED 40 29 24
17Q LOSS WILD-TYPE 306 121 91

Figure S176.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'17q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00155 (Wilcoxon-test), Q value = 0.03

Table S177.  Gene #72: '17q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
17Q LOSS MUTATED 87 3.5 (6.8)
17Q LOSS WILD-TYPE 493 2.0 (4.2)

Figure S177.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'18p loss' versus 'TUMOR_TISSUE_SITE'

P value = 7.77e-07 (Fisher's exact test), Q value = 0.00041

Table S178.  Gene #73: '18p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
18P LOSS MUTATED 251 126
18P LOSS WILD-TYPE 197 36

Figure S178.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'18p loss' versus 'PATHOLOGIC_STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0045

Table S179.  Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
18P LOSS MUTATED 58 0 17 98 5 2 10 12 55 37 50 22 1
18P LOSS WILD-TYPE 46 1 20 74 7 0 14 3 29 18 13 2 1

Figure S179.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'18p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00317 (Fisher's exact test), Q value = 0.047

Table S180.  Gene #73: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
18P LOSS MUTATED 194 106 78
18P LOSS WILD-TYPE 152 44 37

Figure S180.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'18p loss' versus 'PATHOLOGY_M_STAGE'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.00091

Table S181.  Gene #73: '18p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
18P LOSS MUTATED 266 73
18P LOSS WILD-TYPE 187 15

Figure S181.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00089

Table S182.  Gene #73: '18p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
18P LOSS MUTATED 237 11 119 7
18P LOSS WILD-TYPE 145 51 27 6

Figure S182.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0028 (Wilcoxon-test), Q value = 0.042

Table S183.  Gene #73: '18p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
18P LOSS MUTATED 358 2.4 (4.9)
18P LOSS WILD-TYPE 222 1.9 (4.4)

Figure S183.  Get High-res Image Gene #73: '18p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0326 (Wilcoxon-test), Q value = 0.2

Table S184.  Gene #74: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 612 66.3 (12.8)
18Q LOSS MUTATED 407 65.6 (12.2)
18Q LOSS WILD-TYPE 205 67.5 (13.8)

Figure S184.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'TUMOR_TISSUE_SITE'

P value = 4.06e-08 (Fisher's exact test), Q value = 4.3e-05

Table S185.  Gene #74: '18q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
18Q LOSS MUTATED 269 135
18Q LOSS WILD-TYPE 179 27

Figure S185.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'18q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0053

Table S186.  Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
18Q LOSS MUTATED 59 0 21 104 5 2 13 13 59 40 52 22 1
18Q LOSS WILD-TYPE 45 1 16 68 7 0 11 2 25 15 11 2 1

Figure S186.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00023 (Fisher's exact test), Q value = 0.0088

Table S187.  Gene #74: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
18Q LOSS MUTATED 205 113 86
18Q LOSS WILD-TYPE 141 37 29

Figure S187.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'18q loss' versus 'PATHOLOGY_M_STAGE'

P value = 5.81e-05 (Fisher's exact test), Q value = 0.0039

Table S188.  Gene #74: '18q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
18Q LOSS MUTATED 289 75
18Q LOSS WILD-TYPE 164 13

Figure S188.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00089

Table S189.  Gene #74: '18q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
18Q LOSS MUTATED 252 14 124 10
18Q LOSS WILD-TYPE 130 48 22 3

Figure S189.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'18q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000441 (Wilcoxon-test), Q value = 0.014

Table S190.  Gene #74: '18q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
18Q LOSS MUTATED 385 2.4 (4.8)
18Q LOSS WILD-TYPE 195 1.8 (4.6)

Figure S190.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'19p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00091 (Fisher's exact test), Q value = 0.021

Table S191.  Gene #75: '19p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
19P LOSS MUTATED 7 0 2 10 2 1 5 1 5 10 9 7 1
19P LOSS WILD-TYPE 97 1 35 162 10 1 19 14 79 45 54 17 1

Figure S191.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'19p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.0068

Table S192.  Gene #75: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
19P LOSS MUTATED 23 15 24
19P LOSS WILD-TYPE 323 135 91

Figure S192.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'19p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0101 (Fisher's exact test), Q value = 0.1

Table S193.  Gene #75: '19p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
19P LOSS MUTATED 38 16
19P LOSS WILD-TYPE 415 72

Figure S193.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'19p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 6.04e-06 (Wilcoxon-test), Q value = 0.00089

Table S194.  Gene #75: '19p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
19P LOSS MUTATED 58 4.5 (6.0)
19P LOSS WILD-TYPE 522 2.0 (4.5)

Figure S194.  Get High-res Image Gene #75: '19p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'19q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0109 (Fisher's exact test), Q value = 0.11

Table S195.  Gene #76: '19q loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
19Q LOSS MUTATED 7 0 2 11 1 1 5 0 5 8 7 6 1
19Q LOSS WILD-TYPE 97 1 35 161 11 1 19 15 79 47 56 18 1

Figure S195.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'19q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00161 (Fisher's exact test), Q value = 0.03

Table S196.  Gene #76: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
19Q LOSS MUTATED 23 12 21
19Q LOSS WILD-TYPE 323 138 94

Figure S196.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'19q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000446 (Wilcoxon-test), Q value = 0.014

Table S197.  Gene #76: '19q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
19Q LOSS MUTATED 53 4.3 (6.2)
19Q LOSS WILD-TYPE 527 2.0 (4.5)

Figure S197.  Get High-res Image Gene #76: '19q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'21q loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.00156 (Fisher's exact test), Q value = 0.03

Table S198.  Gene #79: '21q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients COLON RECTUM
ALL 448 162
21Q LOSS MUTATED 124 67
21Q LOSS WILD-TYPE 324 95

Figure S198.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0139 (Fisher's exact test), Q value = 0.13

Table S199.  Gene #79: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
21Q LOSS MUTATED 93 51 47
21Q LOSS WILD-TYPE 253 99 68

Figure S199.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00023 (Fisher's exact test), Q value = 0.0088

Table S200.  Gene #79: '21q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
21Q LOSS MUTATED 116 8 62 3
21Q LOSS WILD-TYPE 266 54 84 10

Figure S200.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00702 (Wilcoxon-test), Q value = 0.082

Table S201.  Gene #79: '21q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
21Q LOSS MUTATED 185 3.3 (6.7)
21Q LOSS WILD-TYPE 395 1.7 (3.3)

Figure S201.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'21q loss' versus 'ETHNICITY'

P value = 0.0376 (Fisher's exact test), Q value = 0.21

Table S202.  Gene #79: '21q loss' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 352
21Q LOSS MUTATED 4 110
21Q LOSS WILD-TYPE 1 242

Figure S202.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #13: 'ETHNICITY'

'22q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00209 (Fisher's exact test), Q value = 0.034

Table S203.  Gene #80: '22q loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

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 104 1 37 172 12 2 24 15 84 55 63 24 2
22Q LOSS MUTATED 24 0 10 46 1 0 7 9 29 23 31 11 0
22Q LOSS WILD-TYPE 80 1 27 126 11 2 17 6 55 32 32 13 2

Figure S203.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #4: 'PATHOLOGIC_STAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00089

Table S204.  Gene #80: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
22Q LOSS MUTATED 86 67 46
22Q LOSS WILD-TYPE 260 83 69

Figure S204.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00266 (Fisher's exact test), Q value = 0.04

Table S205.  Gene #80: '22q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
22Q LOSS MUTATED 134 41
22Q LOSS WILD-TYPE 319 47

Figure S205.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0202 (Fisher's exact test), Q value = 0.15

Table S206.  Gene #80: '22q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 382 62 146 13
22Q LOSS MUTATED 134 10 51 4
22Q LOSS WILD-TYPE 248 52 95 9

Figure S206.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000189 (Wilcoxon-test), Q value = 0.0078

Table S207.  Gene #80: '22q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
22Q LOSS MUTATED 190 2.9 (5.1)
22Q LOSS WILD-TYPE 390 1.9 (4.5)

Figure S207.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0324 (Fisher's exact test), Q value = 0.2

Table S208.  Gene #81: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 346 150 115
XP LOSS MUTATED 43 21 26
XP LOSS WILD-TYPE 303 129 89

Figure S208.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'xp loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0176 (Wilcoxon-test), Q value = 0.14

Table S209.  Gene #81: 'xp loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 580 2.2 (4.7)
XP LOSS MUTATED 85 3.2 (5.4)
XP LOSS WILD-TYPE 495 2.1 (4.6)

Figure S209.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'xq loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0164 (Fisher's exact test), Q value = 0.14

Table S210.  Gene #82: 'xq loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 453 88
XQ LOSS MUTATED 53 19
XQ LOSS WILD-TYPE 400 69

Figure S210.  Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/22524545/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/COADREAD-TP/22506534/COADREAD-TP.merged_data.txt

  • Number of patients = 614

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 13

  • Exclude regions 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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