Correlation between copy number variations of arm-level result and selected clinical features
Colon Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1FB51ZD
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1FB51ZD
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 81 arm-level events and 12 clinical features across 443 patients, 206 significant findings detected with Q value < 0.25.

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

  • 2q gain cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • 3p gain cnv correlated to 'NEOPLASM_DISEASESTAGE'.

  • 3q gain cnv correlated to 'NEOPLASM_DISEASESTAGE'.

  • 4p gain cnv correlated to 'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • 4q gain cnv correlated to 'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

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

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

  • 6q gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

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

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

  • 8q gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

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

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

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

  • 10q gain cnv correlated to 'YEARS_TO_BIRTH',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • 11p gain cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • 11q gain cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

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

  • 13q gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'COMPLETENESS_OF_RESECTION', and 'NUMBER_OF_LYMPH_NODES'.

  • 14q gain cnv correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

  • 15q gain cnv correlated to 'COMPLETENESS_OF_RESECTION'.

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

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

  • 17p gain cnv correlated to 'RACE'.

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

  • 18q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 20p gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.

  • 20q gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • 21q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • xp gain cnv correlated to 'PATHOLOGY_T_STAGE'.

  • xq gain cnv correlated to 'PATHOLOGY_T_STAGE'.

  • 1p loss cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 1q loss cnv correlated to 'Time to Death',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 4p loss cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION',  'COMPLETENESS_OF_RESECTION', and 'NUMBER_OF_LYMPH_NODES'.

  • 4q loss cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • 5p loss cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

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

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

  • 6q loss cnv correlated to 'Time to Death',  'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

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

  • 8q loss cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • 9p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

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

  • 10p loss cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • 10q loss cnv correlated to 'PATHOLOGY_M_STAGE'.

  • 11p loss cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 11q loss cnv correlated to 'PATHOLOGY_M_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

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

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

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

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

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

  • 16q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 17p loss cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'COMPLETENESS_OF_RESECTION', and 'NUMBER_OF_LYMPH_NODES'.

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

  • 18p loss cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'COMPLETENESS_OF_RESECTION', and 'NUMBER_OF_LYMPH_NODES'.

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

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

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

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

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

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

  • xq loss cnv correlated to 'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 81 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 206 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		RACE
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test
4p loss 132 (30%) 311 0.0473
(0.233) 		0.835
(1.00) 		0.00248
(0.0394) 		0.272
(0.653) 		0.0009
(0.0211) 		1.38e-05
(0.00191) 		1
(1.00) 		0.0218
(0.153) 		0.026
(0.17) 		0.0285
(0.171) 		0.00044
(0.0147) 		0.79
(1.00)
11p gain 52 (12%) 391 0.907
(1.00) 		0.00427
(0.061) 		0.00542
(0.0702) 		0.0903
(0.36) 		0.011
(0.112) 		0.0138
(0.13) 		1
(1.00) 		0.00762
(0.0892) 		0.0376
(0.2) 		0.231
(0.611) 		0.00684
(0.0834) 		0.578
(0.877)
18p loss 249 (56%) 194 0.7
(0.958) 		0.0271
(0.17) 		0.00044
(0.0147) 		0.934
(1.00) 		0.00395
(0.0573) 		2.25e-05
(0.00243) 		0.339
(0.707) 		1.19e-09
(1.16e-06) 		0.26
(0.638) 		0.0269
(0.17) 		0.00183
(0.0331) 		0.983
(1.00)
11q gain 50 (11%) 393 0.64
(0.919) 		0.000225
(0.00913) 		0.00528
(0.0702) 		0.292
(0.665) 		0.00806
(0.0905) 		0.174
(0.531) 		1
(1.00) 		0.00742
(0.088) 		0.0348
(0.192) 		0.366
(0.737) 		0.00911
(0.0973) 		0.741
(0.98)
13q gain 253 (57%) 190 0.538
(0.846) 		0.553
(0.86) 		0.00053
(0.0156) 		0.986
(1.00) 		0.00324
(0.05) 		0.00193
(0.0337) 		0.387
(0.753) 		2.08e-06
(0.000511) 		0.264
(0.642) 		0.0308
(0.177) 		0.0101
(0.106) 		0.194
(0.564)
4q loss 121 (27%) 322 0.029
(0.173) 		0.862
(1.00) 		0.0152
(0.137) 		0.263
(0.641) 		0.00091
(0.0211) 		0.0044
(0.061) 		0.595
(0.894) 		0.118
(0.42) 		0.02
(0.146) 		0.348
(0.715) 		0.000465
(0.0149) 		0.633
(0.917)
15q loss 153 (35%) 290 0.269
(0.651) 		0.44
(0.793) 		0.0284
(0.171) 		0.655
(0.932) 		0.0315
(0.179) 		0.00116
(0.0252) 		0.765
(0.997) 		0.0284
(0.171) 		0.0407
(0.21) 		0.377
(0.744) 		0.0197
(0.146) 		0.149
(0.485)
17p loss 230 (52%) 213 0.16
(0.504) 		0.0757
(0.323) 		0.0001
(0.00748) 		0.678
(0.941) 		0.00012
(0.00778) 		0.000257
(0.00962) 		0.0577
(0.266) 		1.11e-05
(0.00179) 		0.249
(0.626) 		0.0376
(0.2) 		3.03e-05
(0.00295) 		0.803
(1.00)
18q loss 266 (60%) 177 0.872
(1.00) 		0.0186
(0.143) 		2e-05
(0.00243) 		0.853
(1.00) 		0.00013
(0.00786) 		0.000113
(0.00778) 		0.245
(0.626) 		3.9e-09
(1.9e-06) 		0.279
(0.66) 		0.108
(0.4) 		0.00018
(0.00847) 		0.927
(1.00)
7p gain 244 (55%) 199 0.826
(1.00) 		0.122
(0.429) 		5e-05
(0.00442) 		0.345
(0.714) 		0.00019
(0.00847) 		0.0254
(0.169) 		0.924
(1.00) 		0.0261
(0.17) 		0.256
(0.635) 		0.286
(0.665) 		0.000494
(0.015) 		0.464
(0.801)
20q gain 315 (71%) 128 0.944
(1.00) 		0.206
(0.58) 		0.00184
(0.0331) 		0.309
(0.68) 		0.0134
(0.13) 		0.00208
(0.0355) 		0.294
(0.665) 		2.1e-06
(0.000511) 		0.56
(0.865) 		0.0921
(0.363) 		0.0174
(0.141) 		0.638
(0.918)
1p loss 92 (21%) 351 0.0171
(0.141) 		0.9
(1.00) 		0.017
(0.141) 		0.373
(0.741) 		0.00069
(0.0186) 		0.00109
(0.024) 		0.293
(0.665) 		0.305
(0.675) 		1
(1.00) 		0.42
(0.787) 		0.000257
(0.00962) 		0.423
(0.787)
5q loss 76 (17%) 367 0.0366
(0.198) 		0.27
(0.652) 		0.0341
(0.192) 		0.797
(1.00) 		0.00107
(0.024) 		0.0364
(0.197) 		0.316
(0.685) 		0.271
(0.653) 		0.0776
(0.325) 		0.668
(0.936) 		0.000192
(0.00847) 		0.366
(0.737)
8p loss 139 (31%) 304 0.92
(1.00) 		0.527
(0.837) 		0.0181
(0.141) 		0.228
(0.611) 		0.00163
(0.0317) 		0.000547
(0.0156) 		0.259
(0.638) 		0.0509
(0.244) 		1
(1.00) 		0.0583
(0.266) 		0.00065
(0.0181) 		0.296
(0.665)
22q loss 142 (32%) 301 0.0879
(0.353) 		0.624
(0.906) 		0.00122
(0.0258) 		0.372
(0.741) 		0.00014
(0.00786) 		0.00162
(0.0317) 		1
(1.00) 		0.00474
(0.0649) 		1
(1.00) 		0.429
(0.787) 		0.000146
(0.00786) 		0.381
(0.748)
6q gain 77 (17%) 366 0.491
(0.816) 		0.453
(0.797) 		0.0409
(0.21) 		0.966
(1.00) 		0.0231
(0.159) 		0.273
(0.653) 		0.802
(1.00) 		0.716
(0.966) 		0.00508
(0.0686) 		0.846
(1.00) 		0.0361
(0.197) 		0.891
(1.00)
7q gain 221 (50%) 222 0.9
(1.00) 		0.0689
(0.306) 		0.0178
(0.141) 		0.177
(0.535) 		0.0159
(0.138) 		0.018
(0.141) 		1
(1.00) 		0.0704
(0.308) 		0.623
(0.906) 		0.437
(0.793) 		0.0114
(0.114) 		0.352
(0.716)
9p gain 79 (18%) 364 0.0114
(0.114) 		0.392
(0.757) 		0.0239
(0.163) 		0.488
(0.816) 		0.2
(0.572) 		0.188
(0.559) 		0.711
(0.964) 		0.0171
(0.141) 		1
(1.00) 		0.904
(1.00) 		0.176
(0.534) 		0.0278
(0.171)
16p gain 106 (24%) 337 0.348
(0.715) 		0.155
(0.493) 		0.00558
(0.0714) 		0.935
(1.00) 		0.00387
(0.057) 		0.247
(0.626) 		0.911
(1.00) 		0.00541
(0.0702) 		0.561
(0.865) 		0.901
(1.00) 		0.00244
(0.0394) 		0.433
(0.79)
16q gain 104 (23%) 339 0.319
(0.689) 		0.113
(0.411) 		0.00144
(0.0298) 		0.953
(1.00) 		0.00176
(0.0331) 		0.507
(0.825) 		0.737
(0.977) 		0.00807
(0.0905) 		0.553
(0.86) 		0.744
(0.982) 		0.00236
(0.0388) 		0.44
(0.793)
1q loss 53 (12%) 390 0.0284
(0.171) 		0.713
(0.964) 		0.0895
(0.358) 		0.808
(1.00) 		0.0252
(0.169) 		0.0475
(0.233) 		0.244
(0.624) 		1
(1.00) 		1
(1.00) 		0.481
(0.812) 		0.0145
(0.135) 		0.227
(0.611)
5p loss 57 (13%) 386 0.166
(0.509) 		0.385
(0.751) 		0.00952
(0.101) 		0.287
(0.665) 		0.0257
(0.17) 		0.206
(0.58) 		1
(1.00) 		0.306
(0.675) 		0.0448
(0.224) 		0.551
(0.86) 		0.019
(0.144) 		0.617
(0.904)
6q loss 45 (10%) 398 0.0107
(0.111) 		0.804
(1.00) 		0.678
(0.941) 		0.231
(0.611) 		0.0499
(0.241) 		0.161
(0.504) 		0.53
(0.837) 		0.649
(0.928) 		1
(1.00) 		0.17
(0.522) 		0.00701
(0.0841) 		0.0161
(0.139)
19p loss 39 (9%) 404 0.071
(0.309) 		0.225
(0.608) 		0.0181
(0.141) 		1
(1.00) 		0.00088
(0.0211) 		0.00252
(0.0394) 		0.868
(1.00) 		0.331
(0.701) 		0.242
(0.622) 		0.282
(0.662) 		7.6e-05
(0.00616) 		0.827
(1.00)
4p gain 12 (3%) 431 0.865
(1.00) 		0.257
(0.635) 		0.205
(0.58) 		0.69
(0.951) 		0.0279
(0.171) 		0.164
(0.506) 		0.389
(0.755) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0156
(0.138) 		0.00194
(0.0337)
4q gain 17 (4%) 426 0.451
(0.796) 		0.801
(1.00) 		0.428
(0.787) 		0.951
(1.00) 		0.00845
(0.092) 		0.0579
(0.266) 		0.334
(0.701) 		0.489
(0.816) 		1
(1.00) 		0.331
(0.701) 		0.00635
(0.0802) 		0.0307
(0.177)
6p gain 85 (19%) 358 0.811
(1.00) 		0.678
(0.941) 		0.115
(0.414) 		0.906
(1.00) 		0.0173
(0.141) 		0.483
(0.814) 		0.334
(0.701) 		0.725
(0.967) 		0.00686
(0.0834) 		0.618
(0.904) 		0.0225
(0.157) 		0.312
(0.682)
10p gain 35 (8%) 408 0.0238
(0.163) 		0.412
(0.782) 		0.458
(0.801) 		0.461
(0.801) 		0.0469
(0.233) 		0.426
(0.787) 		0.862
(1.00) 		1
(1.00) 		1
(1.00) 		0.31
(0.68) 		0.0529
(0.25) 		0.163
(0.505)
10q gain 21 (5%) 422 0.756
(0.991) 		0.0347
(0.192) 		0.463
(0.801) 		0.965
(1.00) 		0.0946
(0.367) 		0.718
(0.967) 		0.824
(1.00) 		0.509
(0.825) 		1
(1.00) 		0.673
(0.94) 		0.0267
(0.17) 		0.0411
(0.21)
20p gain 240 (54%) 203 0.333
(0.701) 		0.34
(0.707) 		0.00016
(0.00819) 		0.798
(1.00) 		0.159
(0.504) 		0.000273
(0.00983) 		0.215
(0.595) 		0.000735
(0.0188) 		0.254
(0.632) 		0.0631
(0.283) 		0.0877
(0.353) 		0.984
(1.00)
8q loss 24 (5%) 419 0.789
(1.00) 		0.79
(1.00) 		0.052
(0.247) 		0.24
(0.62) 		0.0174
(0.141) 		0.0298
(0.174) 		0.676
(0.941) 		0.552
(0.86) 		1
(1.00) 		0.787
(1.00) 		0.742
(0.98) 		0.0781
(0.326)
10p loss 67 (15%) 376 0.988
(1.00) 		0.195
(0.565) 		0.0347
(0.192) 		0.965
(1.00) 		0.0818
(0.337) 		0.0184
(0.142) 		0.791
(1.00) 		0.332
(0.701) 		0.0611
(0.276) 		0.529
(0.837) 		0.0318
(0.18) 		0.563
(0.868)
12q loss 48 (11%) 395 0.317
(0.685) 		0.455
(0.799) 		0.164
(0.506) 		0.467
(0.801) 		0.0374
(0.2) 		0.106
(0.398) 		0.76
(0.995) 		0.0442
(0.223) 		1
(1.00) 		0.87
(1.00) 		0.0137
(0.13) 		0.416
(0.784)
17q loss 66 (15%) 377 0.134
(0.449) 		0.897
(1.00) 		0.19
(0.562) 		0.369
(0.741) 		0.0158
(0.138) 		0.0402
(0.209) 		0.79
(1.00) 		0.698
(0.958) 		1
(1.00) 		0.725
(0.967) 		0.000891
(0.0211) 		0.111
(0.406)
19q loss 35 (8%) 408 0.224
(0.605) 		0.373
(0.741) 		0.0829
(0.34) 		0.984
(1.00) 		0.00161
(0.0317) 		0.0164
(0.14) 		0.725
(0.967) 		0.44
(0.793) 		0.219
(0.603) 		0.238
(0.618) 		0.000474
(0.0149) 		0.0788
(0.327)
21q loss 120 (27%) 323 0.738
(0.977) 		0.95
(1.00) 		0.56
(0.865) 		0.464
(0.801) 		0.0196
(0.146) 		0.154
(0.493) 		0.831
(1.00) 		0.00798
(0.0905) 		1
(1.00) 		0.765
(0.997) 		0.0199
(0.146) 		0.342
(0.708)
xp loss 63 (14%) 380 0.207
(0.58) 		0.818
(1.00) 		0.0746
(0.322) 		0.15
(0.485) 		0.00071
(0.0187) 		0.0273
(0.17) 		0.22
(0.603) 		0.427
(0.787) 		1
(1.00) 		0.871
(1.00) 		0.000206
(0.0087) 		0.667
(0.936)
xq loss 51 (12%) 392 0.46
(0.801) 		0.747
(0.984) 		0.161
(0.504) 		0.154
(0.493) 		0.00852
(0.092) 		0.0081
(0.0905) 		0.374
(0.741) 		0.829
(1.00) 		1
(1.00) 		0.493
(0.818) 		0.00386
(0.057) 		0.694
(0.954)
1q gain 79 (18%) 364 0.496
(0.819) 		0.498
(0.82) 		0.22
(0.603) 		0.57
(0.873) 		0.133
(0.448) 		0.00355
(0.0539) 		0.136
(0.451) 		0.103
(0.386) 		0.446
(0.793) 		0.259
(0.638) 		0.0269
(0.17) 		1
(1.00)
2q gain 75 (17%) 368 0.247
(0.626) 		0.476
(0.809) 		0.206
(0.58) 		0.439
(0.793) 		0.0262
(0.17) 		0.572
(0.874) 		0.9
(1.00) 		0.141
(0.465) 		0.428
(0.787) 		0.146
(0.478) 		0.0209
(0.151) 		0.608
(0.898)
5p gain 67 (15%) 376 0.815
(1.00) 		0.0945
(0.367) 		0.296
(0.665) 		0.885
(1.00) 		0.0486
(0.238) 		0.435
(0.79) 		0.289
(0.665) 		0.847
(1.00) 		1
(1.00) 		0.399
(0.762) 		0.031
(0.177) 		0.195
(0.565)
8q gain 223 (50%) 220 0.898
(1.00) 		0.018
(0.141) 		0.572
(0.874) 		0.237
(0.618) 		0.576
(0.876) 		0.267
(0.648) 		0.506
(0.825) 		0.0519
(0.247) 		0.248
(0.626) 		0.543
(0.851) 		0.398
(0.761) 		0.956
(1.00)
9q gain 71 (16%) 372 0.0135
(0.13) 		0.4
(0.763) 		0.21
(0.584) 		0.426
(0.787) 		0.539
(0.846) 		0.182
(0.545) 		1
(1.00) 		0.0228
(0.158) 		1
(1.00) 		0.943
(1.00) 		0.377
(0.744) 		0.0961
(0.371)
12q gain 87 (20%) 356 0.8
(1.00) 		0.118
(0.42) 		0.0155
(0.138) 		0.449
(0.796) 		0.0563
(0.262) 		0.381
(0.748) 		0.72
(0.967) 		0.295
(0.665) 		1
(1.00) 		0.348
(0.715) 		0.0267
(0.17) 		0.65
(0.928)
14q gain 35 (8%) 408 0.803
(1.00) 		0.789
(1.00) 		0.581
(0.879) 		0.807
(1.00) 		0.476
(0.809) 		0.289
(0.665) 		0.601
(0.897) 		0.0391
(0.204) 		1
(1.00) 		0.723
(0.967) 		0.296
(0.665) 		0.0296
(0.174)
18p gain 22 (5%) 421 0.291
(0.665) 		0.503
(0.823) 		0.0947
(0.367) 		0.968
(1.00) 		0.0309
(0.177) 		1
(1.00) 		0.382
(0.748) 		0.0197
(0.146) 		1
(1.00) 		0.527
(0.837) 		0.0543
(0.255) 		0.776
(1.00)
6p loss 33 (7%) 410 0.0215
(0.152) 		0.192
(0.562) 		0.733
(0.976) 		0.125
(0.434) 		0.937
(1.00) 		0.426
(0.787) 		0.37
(0.741) 		0.792
(1.00) 		1
(1.00) 		0.11
(0.406) 		0.948
(1.00) 		0.036
(0.197)
9q loss 50 (11%) 393 0.599
(0.897) 		0.0716
(0.311) 		0.668
(0.936) 		0.113
(0.411) 		0.136
(0.451) 		0.0445
(0.223) 		0.654
(0.932) 		0.0444
(0.223) 		1
(1.00) 		0.477
(0.809) 		0.102
(0.384) 		0.609
(0.899)
11q loss 62 (14%) 381 0.32
(0.691) 		0.413
(0.782) 		0.23
(0.611) 		0.238
(0.618) 		0.0545
(0.255) 		0.0149
(0.135) 		0.495
(0.819) 		1
(1.00) 		1
(1.00) 		0.422
(0.787) 		0.0434
(0.221) 		0.523
(0.837)
12p loss 46 (10%) 397 0.191
(0.562) 		0.333
(0.701) 		0.415
(0.784) 		0.442
(0.793) 		0.0924
(0.363) 		0.161
(0.504) 		1
(1.00) 		0.0117
(0.116) 		0.281
(0.662) 		0.903
(1.00) 		0.0388
(0.204) 		0.881
(1.00)
13q loss 12 (3%) 431 0.337
(0.704) 		1
(1.00) 		0.788
(1.00) 		0.454
(0.797) 		0.11
(0.406) 		0.621
(0.904) 		0.775
(1.00) 		0.178
(0.536) 		1
(1.00) 		0.817
(1.00) 		0.0131
(0.129) 		0.0201
(0.146)
14q loss 134 (30%) 309 0.815
(1.00) 		0.349
(0.716) 		0.192
(0.562) 		0.33
(0.701) 		0.0927
(0.363) 		0.00437
(0.061) 		0.918
(1.00) 		6.16e-06
(0.0012) 		0.557
(0.865) 		0.642
(0.921) 		0.175
(0.532) 		0.93
(1.00)
3p gain 45 (10%) 398 0.144
(0.472) 		0.0974
(0.371) 		0.0023
(0.0385) 		0.871
(1.00) 		0.23
(0.611) 		0.205
(0.58) 		0.639
(0.918) 		0.818
(1.00) 		1
(1.00) 		0.945
(1.00) 		0.127
(0.436) 		0.199
(0.572)
3q gain 64 (14%) 379 0.154
(0.493) 		0.266
(0.647) 		0.0149
(0.135) 		0.62
(0.904) 		0.0764
(0.323) 		0.0977
(0.371) 		0.501
(0.822) 		0.427
(0.787) 		1
(1.00) 		0.9
(1.00) 		0.124
(0.432) 		0.233
(0.613)
15q gain 12 (3%) 431 0.665
(0.936) 		0.293
(0.665) 		0.75
(0.986) 		0.509
(0.825) 		0.719
(0.967) 		0.111
(0.406) 		0.0764
(0.323) 		1
(1.00) 		1
(1.00) 		0.0494
(0.24) 		0.323
(0.694) 		0.306
(0.675)
17p gain 29 (7%) 414 0.0698
(0.307) 		0.615
(0.904) 		0.479
(0.812) 		0.851
(1.00) 		0.33
(0.701) 		0.395
(0.757) 		0.702
(0.958) 		0.573
(0.874) 		1
(1.00) 		0.911
(1.00) 		0.783
(1.00) 		0.0509
(0.244)
18q gain 13 (3%) 430 0.666
(0.936) 		0.0862
(0.349) 		0.45
(0.796) 		0.763
(0.997) 		0.298
(0.667) 		1
(1.00) 		0.582
(0.879) 		0.0214
(0.152) 		1
(1.00) 		1
(1.00) 		0.882
(1.00) 		0.388
(0.753)
21q gain 24 (5%) 419 0.688
(0.951) 		0.00178
(0.0331) 		0.525
(0.837) 		0.12
(0.423) 		0.288
(0.665) 		0.509
(0.825) 		0.534
(0.841) 		0.222
(0.605) 		1
(1.00) 		0.429
(0.787) 		0.139
(0.46) 		0.596
(0.894)
xp gain 66 (15%) 377 0.886
(1.00) 		0.661
(0.936) 		0.433
(0.79) 		0.00666
(0.083) 		0.637
(0.918) 		0.701
(0.958) 		0.23
(0.611) 		0.846
(1.00) 		0.384
(0.751) 		0.934
(1.00) 		0.667
(0.936) 		0.751
(0.986)
xq gain 76 (17%) 367 0.606
(0.897) 		0.717
(0.966) 		0.151
(0.489) 		0.00823
(0.0909) 		0.895
(1.00) 		1
(1.00) 		0.377
(0.744) 		0.465
(0.801) 		0.432
(0.79) 		0.853
(1.00) 		0.851
(1.00) 		0.628
(0.911)
9p loss 51 (12%) 392 0.98
(1.00) 		0.239
(0.618) 		0.944
(1.00) 		0.085
(0.347) 		0.289
(0.665) 		0.279
(0.66) 		0.235
(0.616) 		0.0295
(0.174) 		1
(1.00) 		0.488
(0.816) 		0.0965
(0.371) 		0.673
(0.94)
10q loss 71 (16%) 372 0.703
(0.958) 		0.13
(0.445) 		0.149
(0.485) 		0.943
(1.00) 		0.207
(0.58) 		0.0385
(0.203) 		0.796
(1.00) 		0.19
(0.562) 		0.0682
(0.304) 		0.247
(0.626) 		0.124
(0.433) 		0.667
(0.936)
11p loss 51 (12%) 392 0.395
(0.757) 		0.65
(0.928) 		0.481
(0.812) 		0.821
(1.00) 		0.0591
(0.268) 		0.0809
(0.335) 		0.767
(0.998) 		0.664
(0.936) 		1
(1.00) 		0.444
(0.793) 		0.0146
(0.135) 		0.491
(0.816)
16q loss 27 (6%) 416 0.253
(0.632) 		0.0241
(0.163) 		0.567
(0.871) 		0.735
(0.976) 		0.703
(0.958) 		0.357
(0.724) 		0.693
(0.954) 		0.394
(0.757) 		1
(1.00) 		0.262
(0.641) 		0.615
(0.904) 		0.306
(0.675)
1p gain 34 (8%) 409 0.854
(1.00) 		0.314
(0.685) 		0.884
(1.00) 		0.952
(1.00) 		0.636
(0.918) 		0.173
(0.528) 		0.724
(0.967) 		0.293
(0.665) 		0.213
(0.593) 		0.277
(0.66) 		0.242
(0.622) 		0.395
(0.757)
2p gain 79 (18%) 364 0.456
(0.799) 		0.979
(1.00) 		0.435
(0.79) 		0.529
(0.837) 		0.114
(0.412) 		0.577
(0.876) 		0.804
(1.00) 		0.103
(0.386) 		0.446
(0.793) 		0.0759
(0.323) 		0.0694
(0.307) 		0.844
(1.00)
5q gain 42 (9%) 401 0.501
(0.822) 		0.916
(1.00) 		0.422
(0.787) 		0.844
(1.00) 		0.297
(0.666) 		0.476
(0.809) 		0.52
(0.837) 		0.635
(0.918) 		1
(1.00) 		0.351
(0.716) 		0.974
(1.00) 		0.255
(0.635)
8p gain 130 (29%) 313 0.549
(0.859) 		0.197
(0.568) 		0.657
(0.933) 		0.774
(1.00) 		0.52
(0.837) 		1
(1.00) 		0.917
(1.00) 		0.45
(0.796) 		0.207
(0.58) 		0.472
(0.807) 		0.467
(0.801) 		0.958
(1.00)
12p gain 93 (21%) 350 0.232
(0.612) 		0.328
(0.701) 		0.118
(0.42) 		0.372
(0.741) 		0.287
(0.665) 		0.865
(1.00) 		0.907
(1.00) 		0.614
(0.904) 		1
(1.00) 		0.53
(0.837) 		0.133
(0.448) 		0.964
(1.00)
17q gain 79 (18%) 364 0.123
(0.43) 		0.336
(0.701) 		0.116
(0.415) 		0.358
(0.725) 		0.131
(0.447) 		0.0624
(0.281) 		0.711
(0.964) 		0.208
(0.582) 		0.446
(0.793) 		0.295
(0.665) 		0.618
(0.904) 		0.734
(0.976)
19p gain 74 (17%) 369 0.527
(0.837) 		0.896
(1.00) 		0.606
(0.897) 		0.811
(1.00) 		0.128
(0.44) 		0.558
(0.865) 		0.0753
(0.323) 		0.352
(0.716) 		0.423
(0.787) 		0.317
(0.685) 		0.933
(1.00) 		0.965
(1.00)
19q gain 83 (19%) 360 0.863
(1.00) 		0.83
(1.00) 		0.757
(0.991) 		0.926
(1.00) 		0.191
(0.562) 		0.352
(0.716) 		0.223
(0.605) 		1
(1.00) 		0.464
(0.801) 		0.332
(0.701) 		0.825
(1.00) 		0.859
(1.00)
22q gain 13 (3%) 430 0.528
(0.837) 		0.334
(0.701) 		0.465
(0.801) 		0.295
(0.665) 		0.924
(1.00) 		0.111
(0.406) 		0.582
(0.879) 		0.231
(0.611) 		0.0857
(0.348) 		0.304
(0.675) 		0.491
(0.816) 		0.795
(1.00)
2p loss 6 (1%) 437 0.709
(0.963) 		0.689
(0.951) 		0.223
(0.605) 		0.845
(1.00) 		0.85
(1.00) 		0.595
(0.894) 		0.219
(0.603) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.521
(0.837)
2q loss 7 (2%) 436 0.964
(1.00) 		0.663
(0.936) 		0.281
(0.662) 		1
(1.00) 		1
(1.00) 		0.604
(0.897) 		0.126
(0.434) 		0.601
(0.897) 		1
(1.00) 		1
(1.00) 		0.803
(1.00)
3p loss 52 (12%) 391 0.404
(0.768) 		0.423
(0.787) 		0.251
(0.628) 		0.133
(0.448) 		0.0919
(0.363) 		0.0569
(0.263) 		1
(1.00) 		0.279
(0.66) 		1
(1.00) 		0.823
(1.00) 		0.0977
(0.371) 		0.781
(1.00)
3q loss 32 (7%) 411 0.707
(0.962) 		0.605
(0.897) 		0.676
(0.941) 		0.497
(0.82) 		0.876
(1.00) 		0.186
(0.556) 		0.466
(0.801) 		0.6
(0.897) 		1
(1.00) 		0.864
(1.00) 		0.843
(1.00) 		0.594
(0.894)
7q loss 3 (1%) 440 0.486
(0.816) 		0.141
(0.466) 		0.373
(0.741) 		0.684
(0.948) 		1
(1.00) 		1
(1.00) 		0.606
(0.897) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.507
(0.825) 		1
(1.00)
16p loss 30 (7%) 413 0.155
(0.493) 		0.0768
(0.323) 		0.393
(0.757) 		0.531
(0.839) 		0.567
(0.871) 		0.249
(0.626) 		0.572
(0.874) 		0.275
(0.656) 		1
(1.00) 		0.181
(0.544) 		0.442
(0.793) 		0.3
(0.668)
20p loss 43 (10%) 400 0.516
(0.834) 		0.443
(0.793) 		0.528
(0.837) 		0.909
(1.00) 		0.501
(0.822) 		0.816
(1.00) 		0.873
(1.00) 		0.488
(0.816) 		1
(1.00) 		1
(1.00) 		0.713
(0.964) 		0.806
(1.00)
20q loss 4 (1%) 439 0.314
(0.685) 		0.244
(0.624) 		0.469
(0.802) 		0.776
(1.00) 		0.129
(0.443) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.162
(0.504)
'1q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00355 (Fisher's exact test), Q value = 0.054

Table S1.  Gene #2: '1q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
1Q GAIN MUTATED 50 20
1Q GAIN WILD-TYPE 272 42

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'1q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0269 (Wilcoxon-test), Q value = 0.17

Table S2.  Gene #2: '1q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
1Q GAIN MUTATED 75 2.7 (4.4)
1Q GAIN WILD-TYPE 343 1.9 (4.5)

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'2q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0262 (Fisher's exact test), Q value = 0.17

Table S3.  Gene #4: '2q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
2Q GAIN MUTATED 34 19 21
2Q GAIN WILD-TYPE 223 85 60

Figure S3.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0209 (Wilcoxon-test), Q value = 0.15

Table S4.  Gene #4: '2q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
2Q GAIN MUTATED 72 2.5 (3.6)
2Q GAIN WILD-TYPE 346 2.0 (4.6)

Figure S4.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'3p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0023 (Fisher's exact test), Q value = 0.039

Table S5.  Gene #5: '3p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
3P GAIN MUTATED 6 1 2 9 1 0 3 4 2 6 5 1 2
3P GAIN WILD-TYPE 68 0 26 122 7 1 18 8 54 33 38 17 0

Figure S5.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'3q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.14

Table S6.  Gene #6: '3q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
3Q GAIN MUTATED 8 1 4 13 1 0 4 5 6 7 7 3 2
3Q GAIN WILD-TYPE 66 0 24 118 7 1 17 7 50 32 36 15 0

Figure S6.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'4p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0279 (Fisher's exact test), Q value = 0.17

Table S7.  Gene #7: '4p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
4P GAIN MUTATED 3 4 5
4P GAIN WILD-TYPE 254 100 76

Figure S7.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0156 (Wilcoxon-test), Q value = 0.14

Table S8.  Gene #7: '4p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
4P GAIN MUTATED 12 3.4 (3.7)
4P GAIN WILD-TYPE 406 2.0 (4.5)

Figure S8.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'4p gain' versus 'RACE'

P value = 0.00194 (Fisher's exact test), Q value = 0.034

Table S9.  Gene #7: '4p gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
4P GAIN MUTATED 1 0 5 4
4P GAIN WILD-TYPE 0 11 49 207

Figure S9.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #12: 'RACE'

'4q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00845 (Fisher's exact test), Q value = 0.092

Table S10.  Gene #8: '4q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
4Q GAIN MUTATED 5 4 8
4Q GAIN WILD-TYPE 252 100 73

Figure S10.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00635 (Wilcoxon-test), Q value = 0.08

Table S11.  Gene #8: '4q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
4Q GAIN MUTATED 17 3.3 (3.3)
4Q GAIN WILD-TYPE 401 2.0 (4.5)

Figure S11.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'4q gain' versus 'RACE'

P value = 0.0307 (Fisher's exact test), Q value = 0.18

Table S12.  Gene #8: '4q gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
4Q GAIN MUTATED 1 0 4 7
4Q GAIN WILD-TYPE 0 11 50 204

Figure S12.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #12: 'RACE'

'5p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0486 (Fisher's exact test), Q value = 0.24

Table S13.  Gene #9: '5p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
5P GAIN MUTATED 30 20 17
5P GAIN WILD-TYPE 227 84 64

Figure S13.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.031 (Wilcoxon-test), Q value = 0.18

Table S14.  Gene #9: '5p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
5P GAIN MUTATED 65 2.6 (3.8)
5P GAIN WILD-TYPE 353 2.0 (4.6)

Figure S14.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'6p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0173 (Fisher's exact test), Q value = 0.14

Table S15.  Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
6P GAIN MUTATED 42 18 25
6P GAIN WILD-TYPE 215 86 56

Figure S15.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00686 (Fisher's exact test), Q value = 0.083

Table S16.  Gene #11: '6p gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
6P GAIN MUTATED 3 82
6P GAIN WILD-TYPE 0 358

Figure S16.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'6p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0225 (Wilcoxon-test), Q value = 0.16

Table S17.  Gene #11: '6p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
6P GAIN MUTATED 83 3.1 (4.9)
6P GAIN WILD-TYPE 335 1.8 (4.3)

Figure S17.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'6q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0409 (Fisher's exact test), Q value = 0.21

Table S18.  Gene #12: '6q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
6Q GAIN MUTATED 11 0 2 17 2 0 5 6 9 10 7 6 1
6Q GAIN WILD-TYPE 63 1 26 114 6 1 16 6 47 29 36 12 1

Figure S18.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0231 (Fisher's exact test), Q value = 0.16

Table S19.  Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
6Q GAIN MUTATED 38 16 23
6Q GAIN WILD-TYPE 219 88 58

Figure S19.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00508 (Fisher's exact test), Q value = 0.069

Table S20.  Gene #12: '6q gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
6Q GAIN MUTATED 3 74
6Q GAIN WILD-TYPE 0 366

Figure S20.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'6q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0361 (Wilcoxon-test), Q value = 0.2

Table S21.  Gene #12: '6q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
6Q GAIN MUTATED 75 3.1 (4.9)
6Q GAIN WILD-TYPE 343 1.9 (4.3)

Figure S21.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'7p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0044

Table S22.  Gene #13: '7p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
7P GAIN MUTATED 40 1 14 52 2 0 12 12 37 25 29 13 1
7P GAIN WILD-TYPE 34 0 14 79 6 1 9 0 19 14 14 5 1

Figure S22.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'7p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0085

Table S23.  Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
7P GAIN MUTATED 120 71 52
7P GAIN WILD-TYPE 137 33 29

Figure S23.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0254 (Fisher's exact test), Q value = 0.17

Table S24.  Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
7P GAIN MUTATED 166 42
7P GAIN WILD-TYPE 156 20

Figure S24.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0261 (Fisher's exact test), Q value = 0.17

Table S25.  Gene #13: '7p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
7P GAIN MUTATED 218 25
7P GAIN WILD-TYPE 163 35

Figure S25.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000494 (Wilcoxon-test), Q value = 0.015

Table S26.  Gene #13: '7p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
7P GAIN MUTATED 235 2.4 (4.8)
7P GAIN WILD-TYPE 183 1.7 (4.0)

Figure S26.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'7q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0178 (Fisher's exact test), Q value = 0.14

Table S27.  Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
7Q GAIN MUTATED 38 1 13 48 2 0 11 8 33 22 26 13 1
7Q GAIN WILD-TYPE 36 0 15 83 6 1 10 4 23 17 17 5 1

Figure S27.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'7q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0159 (Fisher's exact test), Q value = 0.14

Table S28.  Gene #14: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
7Q GAIN MUTATED 113 60 47
7Q GAIN WILD-TYPE 144 44 34

Figure S28.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.018 (Fisher's exact test), Q value = 0.14

Table S29.  Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
7Q GAIN MUTATED 148 39
7Q GAIN WILD-TYPE 174 23

Figure S29.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0114 (Wilcoxon-test), Q value = 0.11

Table S30.  Gene #14: '7q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
7Q GAIN MUTATED 214 2.4 (4.8)
7Q GAIN WILD-TYPE 204 1.8 (4.0)

Figure S30.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'8q gain' versus 'YEARS_TO_BIRTH'

P value = 0.018 (Wilcoxon-test), Q value = 0.14

Table S31.  Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
8Q GAIN MUTATED 222 65.7 (12.5)
8Q GAIN WILD-TYPE 219 68.2 (13.4)

Figure S31.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0519 (Fisher's exact test), Q value = 0.25

Table S32.  Gene #16: '8q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
8Q GAIN MUTATED 199 23
8Q GAIN WILD-TYPE 182 37

Figure S32.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'9p gain' versus 'Time to Death'

P value = 0.0114 (logrank test), Q value = 0.11

Table S33.  Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
9P GAIN MUTATED 77 25 0.0 - 98.2 (16.4)
9P GAIN WILD-TYPE 353 68 0.0 - 140.4 (21.4)

Figure S33.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0239 (Fisher's exact test), Q value = 0.16

Table S34.  Gene #17: '9p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
9P GAIN MUTATED 9 1 6 18 2 0 1 4 8 13 8 5 1
9P GAIN WILD-TYPE 65 0 22 113 6 1 20 8 48 26 35 13 1

Figure S34.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0171 (Fisher's exact test), Q value = 0.14

Table S35.  Gene #17: '9p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
9P GAIN MUTATED 61 18
9P GAIN WILD-TYPE 320 42

Figure S35.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'9p gain' versus 'RACE'

P value = 0.0278 (Fisher's exact test), Q value = 0.17

Table S36.  Gene #17: '9p gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
9P GAIN MUTATED 1 1 16 35
9P GAIN WILD-TYPE 0 10 38 176

Figure S36.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #12: 'RACE'

'9q gain' versus 'Time to Death'

P value = 0.0135 (logrank test), Q value = 0.13

Table S37.  Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
9Q GAIN MUTATED 69 23 0.0 - 98.2 (15.0)
9Q GAIN WILD-TYPE 361 70 0.0 - 140.4 (21.4)

Figure S37.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0228 (Fisher's exact test), Q value = 0.16

Table S38.  Gene #18: '9q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
9Q GAIN MUTATED 55 16
9Q GAIN WILD-TYPE 326 44

Figure S38.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'Time to Death'

P value = 0.0238 (logrank test), Q value = 0.16

Table S39.  Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
10P GAIN MUTATED 32 11 0.0 - 91.8 (16.2)
10P GAIN WILD-TYPE 398 82 0.0 - 140.4 (21.3)

Figure S39.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

'10p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0469 (Fisher's exact test), Q value = 0.23

Table S40.  Gene #19: '10p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
10P GAIN MUTATED 16 7 12
10P GAIN WILD-TYPE 241 97 69

Figure S40.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'10p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0529 (Wilcoxon-test), Q value = 0.25

Table S41.  Gene #19: '10p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
10P GAIN MUTATED 33 3.5 (5.3)
10P GAIN WILD-TYPE 385 2.0 (4.4)

Figure S41.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'10q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0347 (Wilcoxon-test), Q value = 0.19

Table S42.  Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
10Q GAIN MUTATED 21 61.0 (12.8)
10Q GAIN WILD-TYPE 420 67.2 (13.0)

Figure S42.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0267 (Wilcoxon-test), Q value = 0.17

Table S43.  Gene #20: '10q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
10Q GAIN MUTATED 19 3.7 (4.5)
10Q GAIN WILD-TYPE 399 2.0 (4.4)

Figure S43.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'10q gain' versus 'RACE'

P value = 0.0411 (Fisher's exact test), Q value = 0.21

Table S44.  Gene #20: '10q gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
10Q GAIN MUTATED 1 1 4 10
10Q GAIN WILD-TYPE 0 10 50 201

Figure S44.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #12: 'RACE'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00427 (Wilcoxon-test), Q value = 0.061

Table S45.  Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
11P GAIN MUTATED 52 61.9 (13.2)
11P GAIN WILD-TYPE 389 67.6 (12.8)

Figure S45.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00542 (Fisher's exact test), Q value = 0.07

Table S46.  Gene #21: '11p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
11P GAIN MUTATED 6 0 2 7 1 0 0 4 10 7 8 5 0
11P GAIN WILD-TYPE 68 1 26 124 7 1 21 8 46 32 35 13 2

Figure S46.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'11p gain' versus 'PATHOLOGY_N_STAGE'

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

Table S47.  Gene #21: '11p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
11P GAIN MUTATED 20 16 15
11P GAIN WILD-TYPE 237 88 66

Figure S47.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0138 (Fisher's exact test), Q value = 0.13

Table S48.  Gene #21: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
11P GAIN MUTATED 30 13
11P GAIN WILD-TYPE 292 49

Figure S48.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00762 (Fisher's exact test), Q value = 0.089

Table S49.  Gene #21: '11p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
11P GAIN MUTATED 50 1
11P GAIN WILD-TYPE 331 59

Figure S49.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0376 (Fisher's exact test), Q value = 0.2

Table S50.  Gene #21: '11p gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
11P GAIN MUTATED 2 50
11P GAIN WILD-TYPE 1 390

Figure S50.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'11p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00684 (Wilcoxon-test), Q value = 0.083

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

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
11P GAIN MUTATED 51 3.5 (7.5)
11P GAIN WILD-TYPE 367 1.9 (3.8)

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

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000225 (Wilcoxon-test), Q value = 0.0091

Table S52.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
11Q GAIN MUTATED 50 60.3 (13.2)
11Q GAIN WILD-TYPE 391 67.8 (12.8)

Figure S52.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00528 (Fisher's exact test), Q value = 0.07

Table S53.  Gene #22: '11q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
11Q GAIN MUTATED 5 0 3 7 1 0 0 4 10 8 5 5 0
11Q GAIN WILD-TYPE 69 1 25 124 7 1 21 8 46 31 38 13 2

Figure S53.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'11q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00806 (Fisher's exact test), Q value = 0.091

Table S54.  Gene #22: '11q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
11Q GAIN MUTATED 19 17 14
11Q GAIN WILD-TYPE 238 87 67

Figure S54.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00742 (Fisher's exact test), Q value = 0.088

Table S55.  Gene #22: '11q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
11Q GAIN MUTATED 49 1
11Q GAIN WILD-TYPE 332 59

Figure S55.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0348 (Fisher's exact test), Q value = 0.19

Table S56.  Gene #22: '11q gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
11Q GAIN MUTATED 2 48
11Q GAIN WILD-TYPE 1 392

Figure S56.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'11q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00911 (Wilcoxon-test), Q value = 0.097

Table S57.  Gene #22: '11q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
11Q GAIN MUTATED 49 3.4 (7.5)
11Q GAIN WILD-TYPE 369 1.9 (3.9)

Figure S57.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'12q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0155 (Fisher's exact test), Q value = 0.14

Table S58.  Gene #24: '12q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
12Q GAIN MUTATED 12 1 7 36 1 0 3 5 6 7 3 6 0
12Q GAIN WILD-TYPE 62 0 21 95 7 1 18 7 50 32 40 12 2

Figure S58.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0267 (Wilcoxon-test), Q value = 0.17

Table S59.  Gene #24: '12q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
12Q GAIN MUTATED 83 1.1 (2.0)
12Q GAIN WILD-TYPE 335 2.3 (4.8)

Figure S59.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'13q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00053 (Fisher's exact test), Q value = 0.016

Table S60.  Gene #25: '13q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
13Q GAIN MUTATED 41 0 14 62 2 1 11 11 34 24 34 14 0
13Q GAIN WILD-TYPE 33 1 14 69 6 0 10 1 22 15 9 4 2

Figure S60.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'13q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00324 (Fisher's exact test), Q value = 0.05

Table S61.  Gene #25: '13q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
13Q GAIN MUTATED 130 70 53
13Q GAIN WILD-TYPE 127 34 28

Figure S61.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'13q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00193 (Fisher's exact test), Q value = 0.034

Table S62.  Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
13Q GAIN MUTATED 176 47
13Q GAIN WILD-TYPE 146 15

Figure S62.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 2.08e-06 (Fisher's exact test), Q value = 0.00051

Table S63.  Gene #25: '13q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
13Q GAIN MUTATED 235 17
13Q GAIN WILD-TYPE 146 43

Figure S63.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'13q gain' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0308 (Fisher's exact test), Q value = 0.18

Table S64.  Gene #25: '13q gain' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
13Q GAIN MUTATED 176 1 18 9
13Q GAIN WILD-TYPE 140 2 6 16

Figure S64.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'13q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0101 (Wilcoxon-test), Q value = 0.11

Table S65.  Gene #25: '13q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
13Q GAIN MUTATED 245 2.2 (3.9)
13Q GAIN WILD-TYPE 173 1.9 (5.2)

Figure S65.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'14q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0391 (Fisher's exact test), Q value = 0.2

Table S66.  Gene #26: '14q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
14Q GAIN MUTATED 26 9
14Q GAIN WILD-TYPE 355 51

Figure S66.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'14q gain' versus 'RACE'

P value = 0.0296 (Fisher's exact test), Q value = 0.17

Table S67.  Gene #26: '14q gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
14Q GAIN MUTATED 1 2 2 19
14Q GAIN WILD-TYPE 0 9 52 192

Figure S67.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #12: 'RACE'

'15q gain' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0494 (Fisher's exact test), Q value = 0.24

Table S68.  Gene #27: '15q gain' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
15Q GAIN MUTATED 7 1 1 1
15Q GAIN WILD-TYPE 309 2 23 24

Figure S68.  Get High-res Image Gene #27: '15q gain' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'16p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00558 (Fisher's exact test), Q value = 0.071

Table S69.  Gene #28: '16p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
16P GAIN MUTATED 12 1 3 25 1 0 6 8 14 14 13 4 1
16P GAIN WILD-TYPE 62 0 25 106 7 1 15 4 42 25 30 14 1

Figure S69.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'16p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00387 (Fisher's exact test), Q value = 0.057

Table S70.  Gene #28: '16p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
16P GAIN MUTATED 47 32 27
16P GAIN WILD-TYPE 210 72 54

Figure S70.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00541 (Fisher's exact test), Q value = 0.07

Table S71.  Gene #28: '16p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
16P GAIN MUTATED 99 6
16P GAIN WILD-TYPE 282 54

Figure S71.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00244 (Wilcoxon-test), Q value = 0.039

Table S72.  Gene #28: '16p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
16P GAIN MUTATED 101 2.6 (4.1)
16P GAIN WILD-TYPE 317 1.9 (4.6)

Figure S72.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'16q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00144 (Fisher's exact test), Q value = 0.03

Table S73.  Gene #29: '16q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
16Q GAIN MUTATED 12 1 3 23 1 0 6 9 17 12 11 4 1
16Q GAIN WILD-TYPE 62 0 25 108 7 1 15 3 39 27 32 14 1

Figure S73.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'16q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00176 (Fisher's exact test), Q value = 0.033

Table S74.  Gene #29: '16q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
16Q GAIN MUTATED 45 33 26
16Q GAIN WILD-TYPE 212 71 55

Figure S74.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00807 (Fisher's exact test), Q value = 0.091

Table S75.  Gene #29: '16q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
16Q GAIN MUTATED 97 6
16Q GAIN WILD-TYPE 284 54

Figure S75.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'16q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00236 (Wilcoxon-test), Q value = 0.039

Table S76.  Gene #29: '16q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
16Q GAIN MUTATED 100 2.6 (4.1)
16Q GAIN WILD-TYPE 318 1.9 (4.5)

Figure S76.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'17p gain' versus 'RACE'

P value = 0.0509 (Fisher's exact test), Q value = 0.24

Table S77.  Gene #30: '17p gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
17P GAIN MUTATED 1 1 6 13
17P GAIN WILD-TYPE 0 10 48 198

Figure S77.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #12: 'RACE'

'18p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0309 (Fisher's exact test), Q value = 0.18

Table S78.  Gene #32: '18p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
18P GAIN MUTATED 10 3 9
18P GAIN WILD-TYPE 247 101 72

Figure S78.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0197 (Fisher's exact test), Q value = 0.15

Table S79.  Gene #32: '18p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
18P GAIN MUTATED 15 7
18P GAIN WILD-TYPE 366 53

Figure S79.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'18q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0214 (Fisher's exact test), Q value = 0.15

Table S80.  Gene #33: '18q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
18Q GAIN MUTATED 8 5
18Q GAIN WILD-TYPE 373 55

Figure S80.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.0082

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

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
20P GAIN MUTATED 41 1 13 61 3 0 9 12 25 21 33 14 1
20P GAIN WILD-TYPE 33 0 15 70 5 1 12 0 31 18 10 4 1

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

'20p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.000273 (Fisher's exact test), Q value = 0.0098

Table S82.  Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
20P GAIN MUTATED 164 47
20P GAIN WILD-TYPE 158 15

Figure S82.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.000735 (Fisher's exact test), Q value = 0.019

Table S83.  Gene #36: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
20P GAIN MUTATED 218 20
20P GAIN WILD-TYPE 163 40

Figure S83.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00184 (Fisher's exact test), Q value = 0.033

Table S84.  Gene #37: '20q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
20Q GAIN MUTATED 53 1 16 84 3 1 13 12 39 31 38 16 1
20Q GAIN WILD-TYPE 21 0 12 47 5 0 8 0 17 8 5 2 1

Figure S84.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0134 (Fisher's exact test), Q value = 0.13

Table S85.  Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
20Q GAIN MUTATED 169 83 62
20Q GAIN WILD-TYPE 88 21 19

Figure S85.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00208 (Fisher's exact test), Q value = 0.035

Table S86.  Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
20Q GAIN MUTATED 220 54
20Q GAIN WILD-TYPE 102 8

Figure S86.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 2.1e-06 (Fisher's exact test), Q value = 0.00051

Table S87.  Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
20Q GAIN MUTATED 287 26
20Q GAIN WILD-TYPE 94 34

Figure S87.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0174 (Wilcoxon-test), Q value = 0.14

Table S88.  Gene #37: '20q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
20Q GAIN MUTATED 300 2.3 (4.8)
20Q GAIN WILD-TYPE 118 1.5 (3.4)

Figure S88.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00178 (Wilcoxon-test), Q value = 0.033

Table S89.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
21Q GAIN MUTATED 24 59.8 (10.0)
21Q GAIN WILD-TYPE 417 67.4 (13.0)

Figure S89.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00666 (Fisher's exact test), Q value = 0.083

Table S90.  Gene #40: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 11 78 301 52
XP GAIN MUTATED 0 14 51 1
XP GAIN WILD-TYPE 11 64 250 51

Figure S90.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00823 (Fisher's exact test), Q value = 0.091

Table S91.  Gene #41: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 11 78 301 52
XQ GAIN MUTATED 0 15 59 2
XQ GAIN WILD-TYPE 11 63 242 50

Figure S91.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1p loss' versus 'Time to Death'

P value = 0.0171 (logrank test), Q value = 0.14

Table S92.  Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
1P LOSS MUTATED 88 25 0.2 - 92.8 (16.7)
1P LOSS WILD-TYPE 342 68 0.0 - 140.4 (21.0)

Figure S92.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.017 (Fisher's exact test), Q value = 0.14

Table S93.  Gene #42: '1p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
1P LOSS MUTATED 9 0 3 23 0 0 5 3 11 11 19 4 0
1P LOSS WILD-TYPE 65 1 25 108 8 1 16 9 45 28 24 14 2

Figure S93.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'1p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00069 (Fisher's exact test), Q value = 0.019

Table S94.  Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
1P LOSS MUTATED 39 25 28
1P LOSS WILD-TYPE 218 79 53

Figure S94.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00109 (Fisher's exact test), Q value = 0.024

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

nPatients 0 1
ALL 322 62
1P LOSS MUTATED 57 23
1P LOSS WILD-TYPE 265 39

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

'1p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000257 (Wilcoxon-test), Q value = 0.0096

Table S96.  Gene #42: '1p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
1P LOSS MUTATED 87 3.7 (6.9)
1P LOSS WILD-TYPE 331 1.7 (3.5)

Figure S96.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'1q loss' versus 'Time to Death'

P value = 0.0284 (logrank test), Q value = 0.17

Table S97.  Gene #43: '1q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
1Q LOSS MUTATED 51 14 0.2 - 91.8 (13.4)
1Q LOSS WILD-TYPE 379 79 0.0 - 140.4 (21.4)

Figure S97.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #1: 'Time to Death'

'1q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0252 (Fisher's exact test), Q value = 0.17

Table S98.  Gene #43: '1q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
1Q LOSS MUTATED 24 12 17
1Q LOSS WILD-TYPE 233 92 64

Figure S98.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0475 (Fisher's exact test), Q value = 0.23

Table S99.  Gene #43: '1q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
1Q LOSS MUTATED 32 12
1Q LOSS WILD-TYPE 290 50

Figure S99.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'1q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0145 (Wilcoxon-test), Q value = 0.13

Table S100.  Gene #43: '1q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
1Q LOSS MUTATED 50 3.4 (4.7)
1Q LOSS WILD-TYPE 368 1.9 (4.4)

Figure S100.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'4p loss' versus 'Time to Death'

P value = 0.0473 (logrank test), Q value = 0.23

Table S101.  Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
4P LOSS MUTATED 127 33 0.2 - 140.4 (20.3)
4P LOSS WILD-TYPE 303 60 0.0 - 139.2 (20.4)

Figure S101.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00248 (Fisher's exact test), Q value = 0.039

Table S102.  Gene #48: '4p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
4P LOSS MUTATED 16 0 4 33 2 0 6 6 14 14 25 7 1
4P LOSS WILD-TYPE 58 1 24 98 6 1 15 6 42 25 18 11 1

Figure S102.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 9e-04 (Fisher's exact test), Q value = 0.021

Table S103.  Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
4P LOSS MUTATED 60 37 35
4P LOSS WILD-TYPE 197 67 46

Figure S103.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'PATHOLOGY_M_STAGE'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0019

Table S104.  Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
4P LOSS MUTATED 79 33
4P LOSS WILD-TYPE 243 29

Figure S104.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0218 (Fisher's exact test), Q value = 0.15

Table S105.  Gene #48: '4p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
4P LOSS MUTATED 121 10
4P LOSS WILD-TYPE 260 50

Figure S105.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.026 (Fisher's exact test), Q value = 0.17

Table S106.  Gene #48: '4p loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
4P LOSS MUTATED 3 129
4P LOSS WILD-TYPE 0 311

Figure S106.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'4p loss' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0285 (Fisher's exact test), Q value = 0.17

Table S107.  Gene #48: '4p loss' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
4P LOSS MUTATED 90 0 13 5
4P LOSS WILD-TYPE 226 3 11 20

Figure S107.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'4p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00044 (Wilcoxon-test), Q value = 0.015

Table S108.  Gene #48: '4p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
4P LOSS MUTATED 127 3.0 (4.7)
4P LOSS WILD-TYPE 291 1.7 (4.3)

Figure S108.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'4q loss' versus 'Time to Death'

P value = 0.029 (logrank test), Q value = 0.17

Table S109.  Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
4Q LOSS MUTATED 118 32 0.2 - 140.4 (20.2)
4Q LOSS WILD-TYPE 312 61 0.0 - 139.2 (20.5)

Figure S109.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0152 (Fisher's exact test), Q value = 0.14

Table S110.  Gene #49: '4q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
4Q LOSS MUTATED 13 0 4 31 1 0 5 6 16 16 20 6 0
4Q LOSS WILD-TYPE 61 1 24 100 7 1 16 6 40 23 23 12 2

Figure S110.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

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

Table S111.  Gene #49: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
4Q LOSS MUTATED 53 37 31
4Q LOSS WILD-TYPE 204 67 50

Figure S111.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0044 (Fisher's exact test), Q value = 0.061

Table S112.  Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
4Q LOSS MUTATED 76 26
4Q LOSS WILD-TYPE 246 36

Figure S112.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

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

Table S113.  Gene #49: '4q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
4Q LOSS MUTATED 3 118
4Q LOSS WILD-TYPE 0 322

Figure S113.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'4q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000465 (Wilcoxon-test), Q value = 0.015

Table S114.  Gene #49: '4q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
4Q LOSS MUTATED 116 3.0 (4.8)
4Q LOSS WILD-TYPE 302 1.7 (4.3)

Figure S114.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'5p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00952 (Fisher's exact test), Q value = 0.1

Table S115.  Gene #50: '5p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
5P LOSS MUTATED 9 0 3 8 0 1 2 4 9 8 5 6 0
5P LOSS WILD-TYPE 65 1 25 123 8 0 19 8 47 31 38 12 2

Figure S115.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'5p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0257 (Fisher's exact test), Q value = 0.17

Table S116.  Gene #50: '5p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
5P LOSS MUTATED 24 19 14
5P LOSS WILD-TYPE 233 85 67

Figure S116.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0448 (Fisher's exact test), Q value = 0.22

Table S117.  Gene #50: '5p loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
5P LOSS MUTATED 2 55
5P LOSS WILD-TYPE 1 385

Figure S117.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'5p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.019 (Wilcoxon-test), Q value = 0.14

Table S118.  Gene #50: '5p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
5P LOSS MUTATED 55 3.3 (6.0)
5P LOSS WILD-TYPE 363 1.9 (4.2)

Figure S118.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'5q loss' versus 'Time to Death'

P value = 0.0366 (logrank test), Q value = 0.2

Table S119.  Gene #51: '5q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
5Q LOSS MUTATED 74 22 0.2 - 91.8 (20.9)
5Q LOSS WILD-TYPE 356 71 0.0 - 140.4 (20.4)

Figure S119.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #1: 'Time to Death'

'5q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0341 (Fisher's exact test), Q value = 0.19

Table S120.  Gene #51: '5q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
5Q LOSS MUTATED 10 0 3 14 0 0 3 4 10 13 10 6 0
5Q LOSS WILD-TYPE 64 1 25 117 8 1 18 8 46 26 33 12 2

Figure S120.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00107 (Fisher's exact test), Q value = 0.024

Table S121.  Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
5Q LOSS MUTATED 32 19 25
5Q LOSS WILD-TYPE 225 85 56

Figure S121.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0364 (Fisher's exact test), Q value = 0.2

Table S122.  Gene #51: '5q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
5Q LOSS MUTATED 46 16
5Q LOSS WILD-TYPE 276 46

Figure S122.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'5q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000192 (Wilcoxon-test), Q value = 0.0085

Table S123.  Gene #51: '5q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
5Q LOSS MUTATED 72 3.7 (5.7)
5Q LOSS WILD-TYPE 346 1.7 (4.1)

Figure S123.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'6p loss' versus 'Time to Death'

P value = 0.0215 (logrank test), Q value = 0.15

Table S124.  Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
6P LOSS MUTATED 32 10 2.0 - 45.4 (17.9)
6P LOSS WILD-TYPE 398 83 0.0 - 140.4 (21.1)

Figure S124.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'RACE'

P value = 0.036 (Fisher's exact test), Q value = 0.2

Table S125.  Gene #52: '6p loss' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
6P LOSS MUTATED 0 3 1 17
6P LOSS WILD-TYPE 1 8 53 194

Figure S125.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #12: 'RACE'

'6q loss' versus 'Time to Death'

P value = 0.0107 (logrank test), Q value = 0.11

Table S126.  Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
6Q LOSS MUTATED 44 13 0.5 - 61.0 (14.5)
6Q LOSS WILD-TYPE 386 80 0.0 - 140.4 (21.6)

Figure S126.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0499 (Fisher's exact test), Q value = 0.24

Table S127.  Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
6Q LOSS MUTATED 20 11 14
6Q LOSS WILD-TYPE 237 93 67

Figure S127.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00701 (Wilcoxon-test), Q value = 0.084

Table S128.  Gene #53: '6q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
6Q LOSS MUTATED 40 3.2 (4.3)
6Q LOSS WILD-TYPE 378 2.0 (4.5)

Figure S128.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'6q loss' versus 'RACE'

P value = 0.0161 (Fisher's exact test), Q value = 0.14

Table S129.  Gene #53: '6q loss' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
6Q LOSS MUTATED 1 3 3 19
6Q LOSS WILD-TYPE 0 8 51 192

Figure S129.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #12: 'RACE'

'8p loss' versus 'NEOPLASM_DISEASESTAGE'

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

Table S130.  Gene #55: '8p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
8P LOSS MUTATED 16 0 6 34 2 0 9 6 16 15 22 9 1
8P LOSS WILD-TYPE 58 1 22 97 6 1 12 6 40 24 21 9 1

Figure S130.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'8p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00163 (Fisher's exact test), Q value = 0.032

Table S131.  Gene #55: '8p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
8P LOSS MUTATED 65 37 37
8P LOSS WILD-TYPE 192 67 44

Figure S131.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000547 (Fisher's exact test), Q value = 0.016

Table S132.  Gene #55: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
8P LOSS MUTATED 91 32
8P LOSS WILD-TYPE 231 30

Figure S132.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0509 (Fisher's exact test), Q value = 0.24

Table S133.  Gene #55: '8p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
8P LOSS MUTATED 126 12
8P LOSS WILD-TYPE 255 48

Figure S133.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00065 (Wilcoxon-test), Q value = 0.018

Table S134.  Gene #55: '8p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
8P LOSS MUTATED 134 3.0 (5.8)
8P LOSS WILD-TYPE 284 1.7 (3.6)

Figure S134.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'8q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.052 (Fisher's exact test), Q value = 0.25

Table S135.  Gene #56: '8q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
8Q LOSS MUTATED 1 0 1 8 2 0 0 1 0 3 5 1 0
8Q LOSS WILD-TYPE 73 1 27 123 6 1 21 11 56 36 38 17 2

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

'8q loss' versus 'PATHOLOGY_N_STAGE'

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

Table S136.  Gene #56: '8q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
8Q LOSS MUTATED 15 1 8
8Q LOSS WILD-TYPE 242 103 73

Figure S136.  Get High-res Image Gene #56: '8q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0298 (Fisher's exact test), Q value = 0.17

Table S137.  Gene #56: '8q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
8Q LOSS MUTATED 10 6
8Q LOSS WILD-TYPE 312 56

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

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0295 (Fisher's exact test), Q value = 0.17

Table S138.  Gene #57: '9p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
9P LOSS MUTATED 49 2
9P LOSS WILD-TYPE 332 58

Figure S138.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0445 (Fisher's exact test), Q value = 0.22

Table S139.  Gene #58: '9q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
9Q LOSS MUTATED 31 12
9Q LOSS WILD-TYPE 291 50

Figure S139.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0444 (Fisher's exact test), Q value = 0.22

Table S140.  Gene #58: '9q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
9Q LOSS MUTATED 47 2
9Q LOSS WILD-TYPE 334 58

Figure S140.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0347 (Fisher's exact test), Q value = 0.19

Table S141.  Gene #59: '10p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
10P LOSS MUTATED 10 0 5 11 0 1 2 3 9 8 12 3 1
10P LOSS WILD-TYPE 64 1 23 120 8 0 19 9 47 31 31 15 1

Figure S141.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'10p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0184 (Fisher's exact test), Q value = 0.14

Table S142.  Gene #59: '10p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
10P LOSS MUTATED 42 16
10P LOSS WILD-TYPE 280 46

Figure S142.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'10p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0318 (Wilcoxon-test), Q value = 0.18

Table S143.  Gene #59: '10p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
10P LOSS MUTATED 64 2.4 (3.4)
10P LOSS WILD-TYPE 354 2.0 (4.6)

Figure S143.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'10q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0385 (Fisher's exact test), Q value = 0.2

Table S144.  Gene #60: '10q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
10Q LOSS MUTATED 47 16
10Q LOSS WILD-TYPE 275 46

Figure S144.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11p loss' versus 'NUMBER_OF_LYMPH_NODES'

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

Table S145.  Gene #61: '11p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
11P LOSS MUTATED 48 2.9 (4.6)
11P LOSS WILD-TYPE 370 2.0 (4.4)

Figure S145.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'11q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.14

Table S146.  Gene #62: '11q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
11Q LOSS MUTATED 38 15
11Q LOSS WILD-TYPE 284 47

Figure S146.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0434 (Wilcoxon-test), Q value = 0.22

Table S147.  Gene #62: '11q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
11Q LOSS MUTATED 59 2.5 (4.3)
11Q LOSS WILD-TYPE 359 2.0 (4.5)

Figure S147.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0117 (Fisher's exact test), Q value = 0.12

Table S148.  Gene #63: '12p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
12P LOSS MUTATED 45 1
12P LOSS WILD-TYPE 336 59

Figure S148.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'12p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0388 (Wilcoxon-test), Q value = 0.2

Table S149.  Gene #63: '12p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
12P LOSS MUTATED 44 2.5 (3.7)
12P LOSS WILD-TYPE 374 2.0 (4.5)

Figure S149.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'12q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0374 (Fisher's exact test), Q value = 0.2

Table S150.  Gene #64: '12q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
12Q LOSS MUTATED 20 15 13
12Q LOSS WILD-TYPE 237 89 68

Figure S150.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0442 (Fisher's exact test), Q value = 0.22

Table S151.  Gene #64: '12q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
12Q LOSS MUTATED 46 2
12Q LOSS WILD-TYPE 335 58

Figure S151.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0137 (Wilcoxon-test), Q value = 0.13

Table S152.  Gene #64: '12q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
12Q LOSS MUTATED 45 2.7 (3.8)
12Q LOSS WILD-TYPE 373 2.0 (4.5)

Figure S152.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0131 (Wilcoxon-test), Q value = 0.13

Table S153.  Gene #65: '13q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
13Q LOSS MUTATED 9 10.6 (15.8)
13Q LOSS WILD-TYPE 409 1.9 (3.7)

Figure S153.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'RACE'

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

Table S154.  Gene #65: '13q loss' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
13Q LOSS MUTATED 1 1 1 6
13Q LOSS WILD-TYPE 0 10 53 205

Figure S154.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #12: 'RACE'

'14q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00437 (Fisher's exact test), Q value = 0.061

Table S155.  Gene #66: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
14Q LOSS MUTATED 90 29
14Q LOSS WILD-TYPE 232 33

Figure S155.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 6.16e-06 (Fisher's exact test), Q value = 0.0012

Table S156.  Gene #66: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
14Q LOSS MUTATED 128 4
14Q LOSS WILD-TYPE 253 56

Figure S156.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0284 (Fisher's exact test), Q value = 0.17

Table S157.  Gene #67: '15q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
15Q LOSS MUTATED 23 0 6 37 2 0 5 7 18 18 22 10 1
15Q LOSS WILD-TYPE 51 1 22 94 6 1 16 5 38 21 21 8 1

Figure S157.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0315 (Fisher's exact test), Q value = 0.18

Table S158.  Gene #67: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
15Q LOSS MUTATED 76 43 34
15Q LOSS WILD-TYPE 181 61 47

Figure S158.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00116 (Fisher's exact test), Q value = 0.025

Table S159.  Gene #67: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
15Q LOSS MUTATED 99 33
15Q LOSS WILD-TYPE 223 29

Figure S159.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0284 (Fisher's exact test), Q value = 0.17

Table S160.  Gene #67: '15q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
15Q LOSS MUTATED 138 13
15Q LOSS WILD-TYPE 243 47

Figure S160.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0407 (Fisher's exact test), Q value = 0.21

Table S161.  Gene #67: '15q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
15Q LOSS MUTATED 3 150
15Q LOSS WILD-TYPE 0 290

Figure S161.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'15q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0197 (Wilcoxon-test), Q value = 0.15

Table S162.  Gene #67: '15q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
15Q LOSS MUTATED 145 2.3 (3.8)
15Q LOSS WILD-TYPE 273 1.9 (4.8)

Figure S162.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0241 (Wilcoxon-test), Q value = 0.16

Table S163.  Gene #69: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
16Q LOSS MUTATED 27 62.0 (11.8)
16Q LOSS WILD-TYPE 414 67.3 (13.0)

Figure S163.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.0075

Table S164.  Gene #70: '17p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
17P LOSS MUTATED 32 0 13 54 1 1 11 10 30 26 32 12 2
17P LOSS WILD-TYPE 42 1 15 77 7 0 10 2 26 13 11 6 0

Figure S164.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0078

Table S165.  Gene #70: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
17P LOSS MUTATED 112 63 54
17P LOSS WILD-TYPE 145 41 27

Figure S165.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000257 (Fisher's exact test), Q value = 0.0096

Table S166.  Gene #70: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
17P LOSS MUTATED 156 46
17P LOSS WILD-TYPE 166 16

Figure S166.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0018

Table S167.  Gene #70: '17p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
17P LOSS MUTATED 213 15
17P LOSS WILD-TYPE 168 45

Figure S167.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0376 (Fisher's exact test), Q value = 0.2

Table S168.  Gene #70: '17p loss' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
17P LOSS MUTATED 159 1 17 8
17P LOSS WILD-TYPE 157 2 7 17

Figure S168.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'17p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 3.03e-05 (Wilcoxon-test), Q value = 0.0029

Table S169.  Gene #70: '17p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
17P LOSS MUTATED 218 2.8 (5.5)
17P LOSS WILD-TYPE 200 1.3 (2.8)

Figure S169.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'17q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0158 (Fisher's exact test), Q value = 0.14

Table S170.  Gene #71: '17q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
17Q LOSS MUTATED 28 20 18
17Q LOSS WILD-TYPE 229 84 63

Figure S170.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0402 (Fisher's exact test), Q value = 0.21

Table S171.  Gene #71: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
17Q LOSS MUTATED 38 14
17Q LOSS WILD-TYPE 284 48

Figure S171.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000891 (Wilcoxon-test), Q value = 0.021

Table S172.  Gene #71: '17q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
17Q LOSS MUTATED 62 3.6 (7.2)
17Q LOSS WILD-TYPE 356 1.8 (3.7)

Figure S172.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0271 (Wilcoxon-test), Q value = 0.17

Table S173.  Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
18P LOSS MUTATED 249 66.0 (12.2)
18P LOSS WILD-TYPE 192 68.2 (13.9)

Figure S173.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00044 (Fisher's exact test), Q value = 0.015

Table S174.  Gene #72: '18p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
18P LOSS MUTATED 37 0 11 64 2 1 9 9 35 25 34 15 1
18P LOSS WILD-TYPE 37 1 17 67 6 0 12 3 21 14 9 3 1

Figure S174.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'18p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00395 (Fisher's exact test), Q value = 0.057

Table S175.  Gene #72: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
18P LOSS MUTATED 127 68 53
18P LOSS WILD-TYPE 130 36 28

Figure S175.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18p loss' versus 'PATHOLOGY_M_STAGE'

P value = 2.25e-05 (Fisher's exact test), Q value = 0.0024

Table S176.  Gene #72: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
18P LOSS MUTATED 168 50
18P LOSS WILD-TYPE 154 12

Figure S176.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1.19e-09 (Fisher's exact test), Q value = 1.2e-06

Table S177.  Gene #72: '18p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
18P LOSS MUTATED 235 12
18P LOSS WILD-TYPE 146 48

Figure S177.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0269 (Fisher's exact test), Q value = 0.17

Table S178.  Gene #72: '18p loss' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
18P LOSS MUTATED 173 0 18 11
18P LOSS WILD-TYPE 143 3 6 14

Figure S178.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'18p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00183 (Wilcoxon-test), Q value = 0.033

Table S179.  Gene #72: '18p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
18P LOSS MUTATED 235 2.5 (5.1)
18P LOSS WILD-TYPE 183 1.6 (3.4)

Figure S179.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0186 (Wilcoxon-test), Q value = 0.14

Table S180.  Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
18Q LOSS MUTATED 266 65.9 (12.3)
18Q LOSS WILD-TYPE 175 68.5 (13.9)

Figure S180.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0024

Table S181.  Gene #73: '18q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
18Q LOSS MUTATED 37 0 14 68 2 1 10 11 37 29 35 15 1
18Q LOSS WILD-TYPE 37 1 14 63 6 0 11 1 19 10 8 3 1

Figure S181.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.0079

Table S182.  Gene #73: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
18Q LOSS MUTATED 133 73 59
18Q LOSS WILD-TYPE 124 31 22

Figure S182.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000113 (Fisher's exact test), Q value = 0.0078

Table S183.  Gene #73: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
18Q LOSS MUTATED 183 51
18Q LOSS WILD-TYPE 139 11

Figure S183.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 3.9e-09 (Fisher's exact test), Q value = 1.9e-06

Table S184.  Gene #73: '18q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
18Q LOSS MUTATED 250 15
18Q LOSS WILD-TYPE 131 45

Figure S184.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'18q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00018 (Wilcoxon-test), Q value = 0.0085

Table S185.  Gene #73: '18q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
18Q LOSS MUTATED 252 2.4 (4.7)
18Q LOSS WILD-TYPE 166 1.6 (4.1)

Figure S185.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'19p loss' versus 'NEOPLASM_DISEASESTAGE'

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

Table S186.  Gene #74: '19p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
19P LOSS MUTATED 7 0 1 5 0 0 3 1 3 7 7 4 1
19P LOSS WILD-TYPE 67 1 27 126 8 1 18 11 53 32 36 14 1

Figure S186.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'19p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00088 (Fisher's exact test), Q value = 0.021

Table S187.  Gene #74: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
19P LOSS MUTATED 14 9 16
19P LOSS WILD-TYPE 243 95 65

Figure S187.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00252 (Fisher's exact test), Q value = 0.039

Table S188.  Gene #74: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
19P LOSS MUTATED 21 12
19P LOSS WILD-TYPE 301 50

Figure S188.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 7.6e-05 (Wilcoxon-test), Q value = 0.0062

Table S189.  Gene #74: '19p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
19P LOSS MUTATED 37 4.5 (5.3)
19P LOSS WILD-TYPE 381 1.9 (4.3)

Figure S189.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'19q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00161 (Fisher's exact test), Q value = 0.032

Table S190.  Gene #75: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
19Q LOSS MUTATED 14 6 15
19Q LOSS WILD-TYPE 243 98 66

Figure S190.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19q loss' versus 'PATHOLOGY_M_STAGE'

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

Table S191.  Gene #75: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
19Q LOSS MUTATED 20 10
19Q LOSS WILD-TYPE 302 52

Figure S191.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000474 (Wilcoxon-test), Q value = 0.015

Table S192.  Gene #75: '19q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
19Q LOSS MUTATED 33 4.6 (5.5)
19Q LOSS WILD-TYPE 385 1.9 (4.3)

Figure S192.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'21q loss' versus 'PATHOLOGY_N_STAGE'

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

Table S193.  Gene #78: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
21Q LOSS MUTATED 60 28 32
21Q LOSS WILD-TYPE 197 76 49

Figure S193.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00798 (Fisher's exact test), Q value = 0.091

Table S194.  Gene #78: '21q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
21Q LOSS MUTATED 112 8
21Q LOSS WILD-TYPE 269 52

Figure S194.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'NUMBER_OF_LYMPH_NODES'

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

Table S195.  Gene #78: '21q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
21Q LOSS MUTATED 114 3.2 (6.6)
21Q LOSS WILD-TYPE 304 1.7 (3.2)

Figure S195.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'22q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00122 (Fisher's exact test), Q value = 0.026

Table S196.  Gene #79: '22q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
22Q LOSS MUTATED 17 0 7 32 1 0 6 7 17 20 23 8 0
22Q LOSS WILD-TYPE 57 1 21 99 7 1 15 5 39 19 20 10 2

Figure S196.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.0079

Table S197.  Gene #79: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
22Q LOSS MUTATED 62 43 37
22Q LOSS WILD-TYPE 195 61 44

Figure S197.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00162 (Fisher's exact test), Q value = 0.032

Table S198.  Gene #79: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
22Q LOSS MUTATED 92 31
22Q LOSS WILD-TYPE 230 31

Figure S198.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00474 (Fisher's exact test), Q value = 0.065

Table S199.  Gene #79: '22q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
22Q LOSS MUTATED 132 10
22Q LOSS WILD-TYPE 249 50

Figure S199.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000146 (Wilcoxon-test), Q value = 0.0079

Table S200.  Gene #79: '22q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
22Q LOSS MUTATED 134 2.9 (5.0)
22Q LOSS WILD-TYPE 284 1.7 (4.1)

Figure S200.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00071 (Fisher's exact test), Q value = 0.019

Table S201.  Gene #80: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
XP LOSS MUTATED 24 18 21
XP LOSS WILD-TYPE 233 86 60

Figure S201.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xp loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0273 (Fisher's exact test), Q value = 0.17

Table S202.  Gene #80: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
XP LOSS MUTATED 40 15
XP LOSS WILD-TYPE 282 47

Figure S202.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'xp loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000206 (Wilcoxon-test), Q value = 0.0087

Table S203.  Gene #80: 'xp loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
XP LOSS MUTATED 60 3.3 (4.5)
XP LOSS WILD-TYPE 358 1.9 (4.4)

Figure S203.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'xq loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00852 (Fisher's exact test), Q value = 0.092

Table S204.  Gene #81: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
XQ LOSS MUTATED 20 15 16
XQ LOSS WILD-TYPE 237 89 65

Figure S204.  Get High-res Image Gene #81: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xq loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0081 (Fisher's exact test), Q value = 0.091

Table S205.  Gene #81: 'xq loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
XQ LOSS MUTATED 31 14
XQ LOSS WILD-TYPE 291 48

Figure S205.  Get High-res Image Gene #81: 'xq loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'xq loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00386 (Wilcoxon-test), Q value = 0.057

Table S206.  Gene #81: 'xq loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
XQ LOSS MUTATED 47 3.0 (4.5)
XQ LOSS WILD-TYPE 371 2.0 (4.4)

Figure S206.  Get High-res Image Gene #81: 'xq loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

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/COAD-TP/15082917/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/COAD-TP/15076851/COAD-TP.merged_data.txt

  • Number of patients = 443

  • Number of significantly arm-level cnvs = 81

  • Number of selected clinical features = 12

  • 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.

Download Results

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

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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