Correlation between copy number variations of arm-level result and selected clinical features
Colorectal Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1C8289B
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/C1C8289B
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 13 clinical features across 608 patients, 226 significant findings detected with Q value < 0.25.

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

  • 2p gain cnv correlated to 'PRIMARY_SITE_OF_DISEASE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'COMPLETENESS_OF_RESECTION'.

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

  • 3p gain cnv correlated to 'PRIMARY_SITE_OF_DISEASE' and 'NEOPLASM_DISEASESTAGE'.

  • 3q gain cnv correlated to 'PRIMARY_SITE_OF_DISEASE',  'NEOPLASM_DISEASESTAGE', and 'PATHOLOGY_M_STAGE'.

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

  • 5q gain cnv correlated to 'PRIMARY_SITE_OF_DISEASE'.

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

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

  • 8p gain cnv correlated to 'COMPLETENESS_OF_RESECTION'.

  • 8q gain cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_M_STAGE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'COMPLETENESS_OF_RESECTION'.

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

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

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

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

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

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

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

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

  • 14q gain cnv correlated to 'RACE'.

  • 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 'Time to Death' and 'RACE'.

  • 17q gain cnv correlated to 'PATHOLOGY_M_STAGE'.

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

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

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

  • 21q gain cnv correlated to 'YEARS_TO_BIRTH'.

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

  • 1q loss cnv correlated to 'PATHOLOGY_M_STAGE'.

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

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

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

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

  • 4q loss cnv correlated to 'PRIMARY_SITE_OF_DISEASE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE',  '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 'PRIMARY_SITE_OF_DISEASE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

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

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

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

  • 8q loss cnv correlated to 'GENDER'.

  • 9p loss cnv correlated to 'PATHOLOGY_M_STAGE' and 'COMPLETENESS_OF_RESECTION'.

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

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

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

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

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

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

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

  • 14q loss cnv correlated to 'PRIMARY_SITE_OF_DISEASE',  'PATHOLOGY_N_STAGE',  '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'.

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

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

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

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

  • 22q loss cnv correlated to 'Time to Death',  '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_M_STAGE'.

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 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 226 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PRIMARY
SITE
OF
DISEASE 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		RACE
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test
18p loss 374 (62%) 234 0.462
(0.744) 		0.0264
(0.165) 		4.65e-07
(0.000245) 		0.0001
(0.00479) 		0.825
(0.947) 		0.003
(0.0416) 		4.99e-06
(0.00081) 		0.559
(0.791) 		1e-05
(0.00081) 		0.164
(0.466) 		0.0236
(0.155) 		0.00191
(0.0335) 		0.777
(0.928)
18q loss 404 (66%) 204 0.708
(0.887) 		0.0158
(0.124) 		3.52e-09
(3.71e-06) 		3e-05
(0.00197) 		0.393
(0.693) 		3e-05
(0.00197) 		8.27e-06
(0.00081) 		0.391
(0.692) 		1e-05
(0.00081) 		0.285
(0.619) 		0.0222
(0.152) 		5.81e-05
(0.00322) 		0.55
(0.782)
20q gain 459 (75%) 149 0.688
(0.871) 		0.221
(0.546) 		1.3e-06
(0.000455) 		0.00028
(0.00987) 		0.289
(0.623) 		0.00042
(0.0123) 		0.000868
(0.0186) 		0.299
(0.632) 		1e-05
(0.00081) 		0.696
(0.877) 		0.0176
(0.131) 		0.0023
(0.0367) 		0.237
(0.565)
13q gain 365 (60%) 243 0.805
(0.943) 		0.549
(0.782) 		0.0149
(0.12) 		0.00101
(0.0205) 		0.757
(0.913) 		0.00026
(0.00978) 		0.0304
(0.18) 		0.282
(0.616) 		1e-05
(0.00081) 		0.328
(0.661) 		0.0898
(0.337) 		0.00112
(0.022) 		0.0585
(0.263)
20p gain 349 (57%) 259 0.218
(0.545) 		0.543
(0.779) 		0.0201
(0.141) 		0.00041
(0.0123) 		0.585
(0.812) 		0.046
(0.226) 		0.000785
(0.0176) 		0.189
(0.505) 		1e-05
(0.00081) 		0.314
(0.646) 		0.0817
(0.321) 		0.0265
(0.165) 		0.818
(0.947)
4p loss 192 (32%) 416 0.361
(0.676) 		0.995
(1.00) 		0.168
(0.47) 		0.0248
(0.159) 		0.715
(0.891) 		0.00113
(0.022) 		0.000554
(0.0142) 		0.727
(0.899) 		0.0294
(0.176) 		0.000585
(0.0147) 		0.147
(0.436) 		0.000481
(0.0132) 		0.719
(0.894)
5q loss 119 (20%) 489 0.102
(0.363) 		0.668
(0.86) 		0.0384
(0.202) 		0.117
(0.39) 		0.9
(0.989) 		0.0115
(0.103) 		0.0528
(0.247) 		0.759
(0.914) 		0.0436
(0.222) 		0.00252
(0.0379) 		0.496
(0.761) 		0.00587
(0.0644) 		0.396
(0.694)
8p loss 215 (35%) 393 0.501
(0.764) 		0.902
(0.989) 		0.00284
(0.0405) 		0.04
(0.206) 		0.175
(0.479) 		0.00049
(0.0132) 		0.00664
(0.0714) 		0.0897
(0.337) 		0.00255
(0.0379) 		0.291
(0.625) 		0.112
(0.384) 		0.00011
(0.00502) 		0.455
(0.738)
15q loss 225 (37%) 383 0.575
(0.804) 		0.44
(0.728) 		0.0566
(0.258) 		0.0317
(0.181) 		0.287
(0.621) 		0.00888
(0.0899) 		0.0101
(0.098) 		0.449
(0.735) 		0.0116
(0.103) 		0.0151
(0.12) 		0.834
(0.947) 		0.00272
(0.0397) 		0.213
(0.539)
17p loss 335 (55%) 273 0.264
(0.597) 		0.34
(0.666) 		0.0164
(0.127) 		0.0051
(0.0594) 		0.478
(0.75) 		0.00127
(0.0243) 		0.00197
(0.0336) 		0.222
(0.546) 		1e-05
(0.00081) 		0.197
(0.516) 		0.078
(0.311) 		0.000281
(0.00987) 		0.531
(0.773)
22q loss 199 (33%) 409 0.0261
(0.165) 		0.742
(0.908) 		0.696
(0.877) 		0.00745
(0.0777) 		0.257
(0.594) 		3e-05
(0.00197) 		0.00359
(0.0462) 		0.796
(0.937) 		0.0336
(0.187) 		0.484
(0.755) 		0.431
(0.724) 		8.96e-05
(0.00449) 		0.395
(0.694)
6q gain 111 (18%) 497 0.536
(0.775) 		0.496
(0.761) 		0.283
(0.617) 		0.0144
(0.118) 		0.68
(0.869) 		0.00213
(0.035) 		0.0135
(0.111) 		0.529
(0.773) 		0.0948
(0.348) 		0.00015
(0.00656) 		0.386
(0.688) 		0.00256
(0.0379) 		0.629
(0.837)
7p gain 347 (57%) 261 0.607
(0.826) 		0.202
(0.526) 		0.0947
(0.348) 		0.00017
(0.00716) 		0.916
(0.997) 		4e-05
(0.00248) 		0.0241
(0.157) 		0.623
(0.835) 		0.00037
(0.0122) 		0.313
(0.646) 		0.366
(0.68) 		7.21e-05
(0.0038) 		0.577
(0.805)
7q gain 309 (51%) 299 0.905
(0.989) 		0.204
(0.526) 		0.521
(0.773) 		0.00042
(0.0123) 		0.636
(0.839) 		0.00139
(0.0261) 		0.00937
(0.0931) 		0.745
(0.908) 		0.00487
(0.0579) 		1
(1.00) 		0.453
(0.736) 		0.00282
(0.0405) 		0.346
(0.667)
4q loss 185 (30%) 423 0.627
(0.837) 		0.542
(0.779) 		0.00901
(0.0904) 		0.0742
(0.302) 		0.597
(0.819) 		0.0023
(0.0367) 		0.0709
(0.298) 		0.725
(0.898) 		0.0109
(0.101) 		0.000438
(0.0125) 		0.898
(0.989) 		0.00158
(0.0287) 		0.634
(0.839)
1q gain 116 (19%) 492 0.557
(0.791) 		0.514
(0.773) 		0.414
(0.712) 		0.21
(0.535) 		0.0383
(0.202) 		0.0278
(0.171) 		0.0158
(0.124) 		0.354
(0.674) 		0.178
(0.483) 		0.383
(0.688) 		0.49
(0.758) 		0.00237
(0.037) 		0.785
(0.93)
2p gain 120 (20%) 488 0.644
(0.845) 		0.991
(1.00) 		0.0502
(0.24) 		0.219
(0.546) 		0.468
(0.747) 		0.032
(0.181) 		0.365
(0.68) 		0.36
(0.676) 		0.0037
(0.0469) 		0.39
(0.692) 		0.0256
(0.164) 		0.101
(0.363) 		0.828
(0.947)
2q gain 118 (19%) 490 0.377
(0.681) 		0.581
(0.808) 		0.0107
(0.101) 		0.155
(0.447) 		0.526
(0.773) 		0.0126
(0.108) 		0.449
(0.735) 		0.261
(0.595) 		0.001
(0.0205) 		0.0765
(0.308) 		0.348
(0.667) 		0.044
(0.222) 		0.337
(0.663)
5p gain 103 (17%) 505 0.85
(0.955) 		0.0839
(0.324) 		0.0503
(0.24) 		0.213
(0.539) 		0.466
(0.746) 		0.0194
(0.138) 		0.266
(0.599) 		1
(1.00) 		0.0232
(0.155) 		0.183
(0.494) 		0.23
(0.558) 		0.0129
(0.109) 		0.114
(0.388)
6p gain 124 (20%) 484 0.48
(0.751) 		0.474
(0.75) 		0.17
(0.471) 		0.0374
(0.202) 		0.532
(0.773) 		0.00064
(0.0153) 		0.0556
(0.255) 		0.314
(0.646) 		0.204
(0.526) 		0.000317
(0.0108) 		0.294
(0.626) 		0.000725
(0.0166) 		0.216
(0.542)
8q gain 311 (51%) 297 0.503
(0.764) 		0.0981
(0.358) 		0.52
(0.773) 		0.0464
(0.227) 		0.217
(0.544) 		0.0777
(0.311) 		0.0131
(0.11) 		0.871
(0.968) 		0.0602
(0.265) 		0.0381
(0.202) 		0.0265
(0.165) 		0.0927
(0.344) 		0.922
(0.999)
9p gain 121 (20%) 487 0.00812
(0.083) 		0.826
(0.947) 		0.0384
(0.202) 		0.0121
(0.106) 		0.548
(0.782) 		0.274
(0.612) 		0.657
(0.852) 		0.685
(0.871) 		0.00545
(0.0617) 		1
(1.00) 		0.394
(0.693) 		0.26
(0.595) 		0.0601
(0.265)
12q gain 111 (18%) 497 0.392
(0.693) 		0.0396
(0.205) 		0.123
(0.405) 		0.0289
(0.175) 		0.449
(0.735) 		0.00947
(0.0932) 		0.289
(0.623) 		0.462
(0.744) 		0.238
(0.565) 		1
(1.00) 		0.594
(0.819) 		0.0049
(0.0579) 		0.769
(0.922)
16p gain 146 (24%) 462 0.263
(0.597) 		0.17
(0.471) 		0.83
(0.947) 		0.0177
(0.131) 		1
(1.00) 		0.00239
(0.037) 		0.264
(0.597) 		0.849
(0.955) 		0.00326
(0.0431) 		0.229
(0.557) 		0.738
(0.906) 		0.00324
(0.0431) 		0.442
(0.728)
16q gain 144 (24%) 464 0.454
(0.736) 		0.119
(0.391) 		0.59
(0.817) 		0.00551
(0.0617) 		0.98
(1.00) 		0.0005
(0.0132) 		0.208
(0.531) 		0.849
(0.955) 		0.00326
(0.0431) 		0.227
(0.552) 		0.781
(0.93) 		0.00206
(0.0345) 		0.433
(0.724)
18p gain 33 (5%) 575 0.28
(0.615) 		0.512
(0.773) 		0.841
(0.952) 		0.0171
(0.129) 		0.745
(0.908) 		0.0147
(0.119) 		1
(1.00) 		0.111
(0.383) 		0.0446
(0.223) 		0.397
(0.694) 		1
(1.00) 		0.0134
(0.111) 		0.816
(0.947)
1p loss 135 (22%) 473 0.17
(0.471) 		0.328
(0.661) 		0.0608
(0.266) 		0.0982
(0.358) 		0.785
(0.93) 		0.00435
(0.0533) 		0.016
(0.125) 		0.434
(0.725) 		0.0106
(0.101) 		0.423
(0.719) 		0.672
(0.863) 		0.000658
(0.0154) 		0.336
(0.663)
3p loss 67 (11%) 541 0.0713
(0.298) 		0.686
(0.871) 		0.306
(0.64) 		0.0548
(0.254) 		0.0321
(0.181) 		0.0319
(0.181) 		0.004
(0.0495) 		0.436
(0.727) 		0.069
(0.293) 		0.26
(0.595) 		0.167
(0.47) 		0.0225
(0.153) 		0.372
(0.681)
5p loss 84 (14%) 524 0.433
(0.724) 		0.609
(0.826) 		0.235
(0.564) 		0.0172
(0.13) 		0.856
(0.956) 		0.0397
(0.205) 		0.492
(0.76) 		0.413
(0.712) 		0.318
(0.647) 		0.0247
(0.159) 		0.712
(0.889) 		0.0296
(0.176) 		0.478
(0.75)
6q loss 68 (11%) 540 0.0205
(0.142) 		0.761
(0.915) 		0.377
(0.681) 		0.335
(0.663) 		0.331
(0.661) 		0.0707
(0.298) 		0.343
(0.667) 		0.246
(0.58) 		0.0392
(0.204) 		1
(1.00) 		0.191
(0.508) 		0.0534
(0.249) 		0.00449
(0.0543)
10p loss 100 (16%) 508 0.335
(0.663) 		0.00519
(0.0594) 		0.136
(0.427) 		0.379
(0.683) 		0.837
(0.948) 		0.101
(0.363) 		0.155
(0.447) 		0.828
(0.947) 		0.0227
(0.153) 		0.00795
(0.0821) 		0.985
(1.00) 		0.0195
(0.138) 		0.67
(0.861)
14q loss 202 (33%) 406 0.937
(1.00) 		0.249
(0.585) 		0.0191
(0.138) 		0.38
(0.684) 		0.385
(0.688) 		0.0308
(0.18) 		0.0342
(0.189) 		0.492
(0.76) 		1e-05
(0.00081) 		1
(1.00) 		0.947
(1.00) 		0.188
(0.502) 		1
(1.00)
19p loss 63 (10%) 545 0.0584
(0.263) 		0.258
(0.595) 		0.129
(0.412) 		0.00296
(0.0416) 		0.785
(0.93) 		0.00026
(0.00978) 		0.00328
(0.0431) 		1
(1.00) 		0.14
(0.431) 		0.237
(0.565) 		0.451
(0.736) 		3.85e-06
(0.00081) 		0.936
(1.00)
21q loss 190 (31%) 418 0.913
(0.994) 		0.476
(0.75) 		0.00152
(0.0281) 		0.506
(0.765) 		0.909
(0.991) 		0.0116
(0.103) 		0.704
(0.884) 		0.662
(0.856) 		0.00026
(0.00978) 		0.471
(0.749) 		0.673
(0.863) 		0.00396
(0.0495) 		0.319
(0.648)
3q gain 97 (16%) 511 0.234
(0.562) 		0.302
(0.635) 		0.0444
(0.223) 		0.0381
(0.202) 		0.866
(0.964) 		0.0654
(0.281) 		0.0441
(0.222) 		0.375
(0.681) 		0.0698
(0.295) 		0.641
(0.843) 		0.61
(0.826) 		0.0588
(0.263) 		0.25
(0.585)
9q gain 101 (17%) 507 0.00626
(0.068) 		0.854
(0.956) 		0.268
(0.601) 		0.0493
(0.238) 		0.538
(0.775) 		0.503
(0.764) 		0.525
(0.773) 		0.827
(0.947) 		0.0287
(0.175) 		1
(1.00) 		0.752
(0.913) 		0.522
(0.773) 		0.268
(0.601)
11p gain 84 (14%) 524 0.834
(0.947) 		0.00572
(0.0634) 		0.0234
(0.155) 		0.129
(0.412) 		0.167
(0.47) 		0.178
(0.483) 		0.059
(0.263) 		1
(1.00) 		0.00198
(0.0336) 		0.115
(0.39) 		0.53
(0.773) 		0.111
(0.383) 		0.462
(0.744)
6p loss 45 (7%) 563 0.0126
(0.108) 		0.329
(0.661) 		0.861
(0.961) 		0.345
(0.667) 		0.55
(0.782) 		0.411
(0.71) 		1
(1.00) 		0.538
(0.775) 		0.15
(0.44) 		0.502
(0.764) 		0.0522
(0.245) 		0.352
(0.672) 		0.00514
(0.0594)
10q loss 110 (18%) 498 0.36
(0.676) 		0.0214
(0.147) 		0.0731
(0.301) 		0.62
(0.834) 		0.99
(1.00) 		0.311
(0.646) 		0.545
(0.781) 		0.752
(0.913) 		0.0191
(0.138) 		0.0121
(0.106) 		1
(1.00) 		0.133
(0.42) 		0.756
(0.913)
12p loss 70 (12%) 538 0.125
(0.41) 		0.577
(0.805) 		0.196
(0.516) 		0.538
(0.775) 		0.232
(0.56) 		0.046
(0.226) 		0.185
(0.496) 		0.8
(0.94) 		0.011
(0.102) 		0.0738
(0.301) 		0.904
(0.989) 		0.0469
(0.228) 		0.781
(0.93)
13q loss 20 (3%) 588 0.565
(0.797) 		0.905
(0.989) 		0.2
(0.522) 		0.629
(0.837) 		0.579
(0.806) 		0.0733
(0.301) 		0.155
(0.447) 		1
(1.00) 		0.0344
(0.19) 		1
(1.00) 		1
(1.00) 		0.00702
(0.0747) 		0.0168
(0.129)
19q loss 55 (9%) 553 0.231
(0.558) 		0.609
(0.826) 		0.15
(0.44) 		0.0319
(0.181) 		0.765
(0.919) 		0.00163
(0.0291) 		0.103
(0.366) 		0.398
(0.694) 		0.224
(0.551) 		0.192
(0.509) 		0.831
(0.947) 		0.000625
(0.0153) 		0.138
(0.431)
xp loss 89 (15%) 519 0.385
(0.688) 		0.755
(0.913) 		0.518
(0.773) 		0.432
(0.724) 		0.415
(0.712) 		0.0287
(0.175) 		0.0487
(0.236) 		0.566
(0.798) 		0.286
(0.621) 		1
(1.00) 		0.944
(1.00) 		0.0192
(0.138) 		0.433
(0.724)
3p gain 72 (12%) 536 0.398
(0.694) 		0.112
(0.384) 		0.0317
(0.181) 		0.0169
(0.129) 		0.983
(1.00) 		0.178
(0.483) 		0.0842
(0.324) 		0.316
(0.647) 		0.0928
(0.344) 		1
(1.00) 		0.971
(1.00) 		0.0818
(0.321) 		0.225
(0.552)
10p gain 47 (8%) 561 0.0412
(0.211) 		0.642
(0.844) 		0.732
(0.903) 		0.702
(0.882) 		0.267
(0.601) 		0.0306
(0.18) 		0.495
(0.761) 		0.879
(0.975) 		0.9
(0.989) 		0.518
(0.773) 		0.572
(0.802) 		0.135
(0.426) 		0.142
(0.431)
10q gain 27 (4%) 581 0.811
(0.946) 		0.0551
(0.255) 		0.663
(0.856) 		0.738
(0.906) 		0.661
(0.856) 		0.0611
(0.266) 		0.546
(0.781) 		0.695
(0.877) 		0.829
(0.947) 		0.337
(0.663) 		0.826
(0.947) 		0.0383
(0.202) 		0.038
(0.202)
11q gain 76 (12%) 532 0.332
(0.661) 		5.62e-05
(0.00322) 		0.129
(0.412) 		0.181
(0.49) 		0.559
(0.791) 		0.169
(0.471) 		0.0751
(0.304) 		1
(1.00) 		0.00353
(0.0459) 		0.313
(0.646) 		0.647
(0.846) 		0.116
(0.39) 		0.451
(0.736)
17p gain 38 (6%) 570 0.037
(0.202) 		0.636
(0.839) 		0.85
(0.955) 		0.53
(0.773) 		0.376
(0.681) 		0.806
(0.943) 		0.615
(0.832) 		1
(1.00) 		0.745
(0.908) 		1
(1.00) 		0.939
(1.00) 		0.936
(1.00) 		0.0386
(0.202)
2p loss 17 (3%) 591 0.785
(0.93) 		0.204
(0.526) 		0.00101
(0.0205) 		0.63
(0.837) 		0.819
(0.947) 		0.798
(0.938) 		0.489
(0.758) 		0.806
(0.943) 		0.0101
(0.098) 		0.227
(0.552) 		1
(1.00) 		0.688
(0.871) 		0.152
(0.442)
3q loss 43 (7%) 565 0.347
(0.667) 		0.533
(0.773) 		0.474
(0.75) 		0.16
(0.459) 		0.126
(0.41) 		0.425
(0.721) 		0.0333
(0.187) 		0.206
(0.528) 		0.00732
(0.0771) 		0.128
(0.412) 		0.449
(0.735) 		0.527
(0.773) 		0.347
(0.667)
9p loss 74 (12%) 534 0.525
(0.773) 		0.215
(0.541) 		0.484
(0.755) 		0.77
(0.923) 		0.0824
(0.322) 		0.367
(0.68) 		0.05
(0.24) 		0.172
(0.473) 		0.102
(0.363) 		1
(1.00) 		0.0459
(0.226) 		0.0786
(0.312) 		0.736
(0.905)
9q loss 75 (12%) 533 0.333
(0.662) 		0.0314
(0.181) 		0.484
(0.755) 		0.608
(0.826) 		0.146
(0.436) 		0.37
(0.681) 		0.0203
(0.142) 		0.459
(0.743) 		0.101
(0.363) 		1
(1.00) 		0.0593
(0.263) 		0.204
(0.526) 		0.824
(0.947)
11p loss 74 (12%) 534 0.805
(0.943) 		0.345
(0.667) 		0.328
(0.661) 		0.22
(0.546) 		0.431
(0.724) 		0.0116
(0.103) 		0.279
(0.614) 		0.901
(0.989) 		0.226
(0.552) 		0.301
(0.635) 		0.929
(1.00) 		0.000418
(0.0123) 		0.242
(0.573)
12q loss 70 (12%) 538 0.127
(0.412) 		0.891
(0.986) 		0.473
(0.75) 		0.139
(0.431) 		0.411
(0.71) 		0.0229
(0.153) 		0.0885
(0.336) 		0.899
(0.989) 		0.068
(0.29) 		0.278
(0.614) 		1
(1.00) 		0.0114
(0.103) 		0.287
(0.621)
17q loss 96 (16%) 512 0.128
(0.412) 		0.854
(0.956) 		0.53
(0.773) 		0.0844
(0.324) 		0.0827
(0.323) 		0.0108
(0.101) 		0.132
(0.419) 		0.505
(0.765) 		0.894
(0.988) 		0.639
(0.842) 		0.633
(0.839) 		0.000845
(0.0185) 		0.148
(0.436)
5q gain 64 (11%) 544 0.661
(0.856) 		0.832
(0.947) 		0.0517
(0.245) 		0.368
(0.681) 		0.352
(0.672) 		0.276
(0.613) 		0.438
(0.727) 		0.793
(0.936) 		0.059
(0.263) 		1
(1.00) 		0.369
(0.681) 		0.358
(0.676) 		0.236
(0.565)
8p gain 168 (28%) 440 0.596
(0.819) 		0.314
(0.646) 		0.356
(0.675) 		0.569
(0.8) 		0.903
(0.989) 		0.308
(0.643) 		0.358
(0.676) 		0.928
(1.00) 		0.648
(0.846) 		0.713
(0.889) 		0.0519
(0.245) 		0.388
(0.691) 		1
(1.00)
14q gain 43 (7%) 565 0.505
(0.765) 		0.853
(0.956) 		0.283
(0.617) 		0.603
(0.823) 		0.945
(1.00) 		0.646
(0.846) 		0.345
(0.667) 		1
(1.00) 		0.109
(0.381) 		0.486
(0.755) 		0.651
(0.848) 		0.251
(0.587) 		0.0277
(0.171)
17q gain 108 (18%) 500 0.072
(0.298) 		0.195
(0.515) 		0.811
(0.946) 		0.293
(0.626) 		0.651
(0.848) 		0.464
(0.744) 		0.0183
(0.135) 		1
(1.00) 		0.63
(0.837) 		1
(1.00) 		0.147
(0.436) 		0.82
(0.947) 		0.824
(0.947)
21q gain 34 (6%) 574 0.918
(0.998) 		0.0189
(0.138) 		0.687
(0.871) 		0.757
(0.913) 		0.206
(0.528) 		0.518
(0.773) 		0.417
(0.712) 		0.486
(0.755) 		0.464
(0.744) 		1
(1.00) 		0.834
(0.947) 		0.23
(0.558) 		0.599
(0.82)
1q loss 76 (12%) 532 0.143
(0.431) 		0.173
(0.474) 		0.214
(0.539) 		0.518
(0.773) 		0.972
(1.00) 		0.143
(0.431) 		0.029
(0.175) 		0.11
(0.383) 		0.197
(0.516) 		0.313
(0.646) 		0.549
(0.782) 		0.0717
(0.298) 		0.0905
(0.338)
8q loss 36 (6%) 572 0.641
(0.843) 		0.886
(0.981) 		0.437
(0.727) 		0.409
(0.709) 		0.711
(0.889) 		0.256
(0.594) 		0.417
(0.712) 		0.024
(0.157) 		0.537
(0.775) 		1
(1.00) 		0.619
(0.833) 		0.897
(0.989) 		0.108
(0.379)
xq loss 77 (13%) 531 0.583
(0.809) 		0.863
(0.961) 		0.129
(0.412) 		0.336
(0.663) 		0.761
(0.915) 		0.117
(0.39) 		0.0134
(0.111) 		0.808
(0.944) 		0.147
(0.436) 		1
(1.00) 		0.417
(0.712) 		0.0855
(0.327) 		0.497
(0.761)
1p gain 49 (8%) 559 0.276
(0.613) 		0.92
(0.998) 		0.732
(0.903) 		0.344
(0.667) 		0.511
(0.772) 		0.316
(0.647) 		0.119
(0.391) 		0.375
(0.681) 		0.0669
(0.286) 		0.533
(0.773) 		0.278
(0.614) 		0.0897
(0.337) 		0.632
(0.839)
4p gain 20 (3%) 588 0.957
(1.00) 		0.382
(0.686) 		0.0734
(0.301) 		0.37
(0.681) 		0.375
(0.681) 		0.777
(0.928) 		0.305
(0.64) 		0.171
(0.472) 		0.136
(0.427) 		1
(1.00) 		0.675
(0.864) 		0.82
(0.947) 		0.193
(0.51)
4q gain 21 (3%) 587 0.522
(0.773) 		0.627
(0.837) 		1
(1.00) 		0.675
(0.864) 		0.97
(1.00) 		0.119
(0.391) 		0.102
(0.363) 		0.118
(0.391) 		0.439
(0.728) 		1
(1.00) 		0.618
(0.833) 		0.0996
(0.361) 		0.374
(0.681)
12p gain 127 (21%) 481 0.143
(0.431) 		0.147
(0.436) 		0.91
(0.992) 		0.169
(0.471) 		0.355
(0.674) 		0.152
(0.442) 		0.665
(0.857) 		1
(1.00) 		0.688
(0.871) 		0.404
(0.701) 		0.784
(0.93) 		0.143
(0.431) 		0.878
(0.974)
15q gain 15 (2%) 593 0.998
(1.00) 		0.359
(0.676) 		1
(1.00) 		0.595
(0.819) 		0.0837
(0.324) 		0.721
(0.895) 		0.279
(0.614) 		0.0634
(0.275) 		0.0803
(0.318) 		0.203
(0.526) 		0.701
(0.882) 		0.418
(0.712) 		0.4
(0.695)
18q gain 19 (3%) 589 0.954
(1.00) 		0.0948
(0.348) 		0.793
(0.936) 		0.111
(0.383) 		0.4
(0.695) 		0.329
(0.661) 		0.485
(0.755) 		0.243
(0.574) 		0.0607
(0.266) 		0.25
(0.585) 		0.602
(0.823) 		0.475
(0.75) 		0.177
(0.483)
19p gain 104 (17%) 504 0.442
(0.728) 		0.774
(0.926) 		0.331
(0.661) 		0.933
(1.00) 		0.856
(0.956) 		0.347
(0.667) 		0.341
(0.667) 		0.332
(0.661) 		0.109
(0.381) 		1
(1.00) 		0.293
(0.626) 		0.568
(0.8) 		0.592
(0.818)
19q gain 113 (19%) 495 0.431
(0.724) 		0.746
(0.908) 		0.724
(0.898) 		0.847
(0.955) 		0.984
(1.00) 		0.291
(0.625) 		0.163
(0.465) 		0.532
(0.773) 		0.257
(0.594) 		1
(1.00) 		0.418
(0.712) 		0.734
(0.904) 		0.464
(0.744)
22q gain 23 (4%) 585 0.877
(0.974) 		0.317
(0.647) 		0.09
(0.337) 		0.617
(0.833) 		0.115
(0.39) 		0.277
(0.614) 		0.376
(0.681) 		0.833
(0.947) 		0.104
(0.369) 		0.295
(0.626) 		0.329
(0.661) 		0.113
(0.387) 		0.818
(0.947)
xp gain 98 (16%) 510 0.532
(0.773) 		0.564
(0.797) 		0.213
(0.539) 		0.148
(0.436) 		0.318
(0.647) 		0.172
(0.473) 		0.26
(0.595) 		0.151
(0.441) 		0.13
(0.414) 		1
(1.00) 		0.597
(0.819) 		0.788
(0.933) 		0.746
(0.908)
xq gain 107 (18%) 501 0.841
(0.952) 		0.495
(0.761) 		0.718
(0.894) 		0.16
(0.459) 		0.53
(0.773) 		0.37
(0.681) 		0.755
(0.913) 		0.166
(0.47) 		0.274
(0.612) 		1
(1.00) 		0.972
(1.00) 		0.441
(0.728) 		0.575
(0.804)
2q loss 14 (2%) 594 0.454
(0.736) 		0.501
(0.764) 		0.0644
(0.278) 		0.312
(0.646) 		1
(1.00) 		0.663
(0.856) 		0.141
(0.431) 		0.43
(0.724) 		0.305
(0.64) 		1
(1.00) 		0.844
(0.954) 		0.441
(0.728)
7q loss 4 (1%) 604 0.514
(0.773) 		0.963
(1.00) 		0.293
(0.626) 		0.635
(0.839) 		0.315
(0.647) 		0.821
(0.947) 		1
(1.00) 		0.347
(0.667) 		0.14
(0.431) 		1
(1.00) 		1
(1.00) 		0.299
(0.632)
11q loss 92 (15%) 516 0.257
(0.594) 		0.517
(0.773) 		0.366
(0.68) 		0.495
(0.761) 		0.745
(0.908) 		0.0863
(0.329) 		0.247
(0.581) 		0.572
(0.802) 		0.141
(0.431) 		0.142
(0.431) 		0.982
(1.00) 		0.0559
(0.256) 		0.26
(0.595)
16p loss 40 (7%) 568 0.139
(0.431) 		0.22
(0.546) 		0.856
(0.956) 		0.118
(0.391) 		0.398
(0.694) 		0.362
(0.677) 		0.469
(0.748) 		0.515
(0.773) 		0.539
(0.775) 		1
(1.00) 		0.152
(0.442) 		0.43
(0.724) 		0.264
(0.597)
16q loss 42 (7%) 566 0.373
(0.681) 		0.116
(0.39) 		0.366
(0.68) 		0.386
(0.688) 		0.794
(0.936) 		0.188
(0.502) 		0.814
(0.947) 		0.75
(0.912) 		0.63
(0.837) 		0.477
(0.75) 		0.389
(0.691) 		0.477
(0.75) 		0.221
(0.546)
20p loss 67 (11%) 541 0.528
(0.773) 		0.469
(0.748) 		0.0767
(0.308) 		0.621
(0.834) 		0.814
(0.947) 		0.419
(0.712) 		0.708
(0.887) 		0.7
(0.881) 		0.139
(0.431) 		0.607
(0.826) 		0.592
(0.818) 		0.921
(0.999) 		0.684
(0.871)
20q loss 6 (1%) 602 0.654
(0.851) 		0.167
(0.47) 		0.351
(0.671) 		0.651
(0.848) 		0.618
(0.833) 		0.734
(0.904) 		0.596
(0.819) 		1
(1.00) 		0.355
(0.674) 		1
(1.00) 		1
(1.00) 		0.686
(0.871) 		0.254
(0.593)
'1q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0383 (Fisher's exact test), Q value = 0.2

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

nPatients T1 T2 T3 T4
ALL 20 107 413 66
1Q GAIN MUTATED 4 15 76 21
1Q GAIN WILD-TYPE 16 92 337 45

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

'1q gain' versus 'PATHOLOGY_N_STAGE'

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

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

nPatients N0 N1 N2
ALL 342 149 114
1Q GAIN MUTATED 54 29 31
1Q GAIN WILD-TYPE 288 120 83

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

'1q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0158 (Fisher's exact test), Q value = 0.12

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

nPatients 0 1
ALL 448 86
1Q GAIN MUTATED 77 25
1Q GAIN WILD-TYPE 371 61

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

'1q gain' versus 'NUMBER_OF_LYMPH_NODES'

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

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

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
1Q GAIN MUTATED 111 3.6 (6.1)
1Q GAIN WILD-TYPE 462 1.9 (4.3)

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

'2p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0502 (Fisher's exact test), Q value = 0.24

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

nPatients COLON RECTUM
ALL 442 162
2P GAIN MUTATED 79 41
2P GAIN WILD-TYPE 363 121

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

'2p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.032 (Fisher's exact test), Q value = 0.18

Table S6.  Gene #3: '2p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
2P GAIN MUTATED 57 29 32
2P GAIN WILD-TYPE 285 120 82

Figure S6.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0037 (Fisher's exact test), Q value = 0.047

Table S7.  Gene #3: '2p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
2P GAIN MUTATED 73 6 41 0
2P GAIN WILD-TYPE 308 54 105 13

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'2p gain' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0256 (Fisher's exact test), Q value = 0.16

Table S8.  Gene #3: '2p gain' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 439 5 36 29
2P GAIN MUTATED 84 3 5 10
2P GAIN WILD-TYPE 355 2 31 19

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'2q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0107 (Fisher's exact test), Q value = 0.1

Table S9.  Gene #4: '2q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
2Q GAIN MUTATED 75 43
2Q GAIN WILD-TYPE 367 119

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'2q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0126 (Fisher's exact test), Q value = 0.11

Table S10.  Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
2Q GAIN MUTATED 55 28 33
2Q GAIN WILD-TYPE 287 121 81

Figure S10.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'2q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.001 (Fisher's exact test), Q value = 0.02

Table S11.  Gene #4: '2q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
2Q GAIN MUTATED 69 6 43 0
2Q GAIN WILD-TYPE 312 54 103 13

Figure S11.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'2q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.044 (Wilcoxon-test), Q value = 0.22

Table S12.  Gene #4: '2q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
2Q GAIN MUTATED 111 2.5 (4.1)
2Q GAIN WILD-TYPE 462 2.2 (4.9)

Figure S12.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'3p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0317 (Fisher's exact test), Q value = 0.18

Table S13.  Gene #5: '3p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
3P GAIN MUTATED 44 27
3P GAIN WILD-TYPE 398 135

Figure S13.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'3p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0169 (Fisher's exact test), Q value = 0.13

Table S14.  Gene #5: '3p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
3P GAIN MUTATED 9 1 2 18 1 0 5 5 6 6 9 5 2
3P GAIN WILD-TYPE 95 0 34 153 9 3 21 16 73 48 52 22 0

Figure S14.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'3q gain' versus 'PRIMARY_SITE_OF_DISEASE'

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

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

nPatients COLON RECTUM
ALL 442 162
3Q GAIN MUTATED 62 34
3Q GAIN WILD-TYPE 380 128

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

'3q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0381 (Fisher's exact test), Q value = 0.2

Table S16.  Gene #6: '3q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
3Q GAIN MUTATED 11 1 4 24 1 0 6 6 11 9 12 7 2
3Q GAIN WILD-TYPE 93 0 32 147 9 3 20 15 68 45 49 20 0

Figure S16.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'3q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0441 (Fisher's exact test), Q value = 0.22

Table S17.  Gene #6: '3q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
3Q GAIN MUTATED 59 19
3Q GAIN WILD-TYPE 389 67

Figure S17.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'5p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0503 (Fisher's exact test), Q value = 0.24

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

nPatients COLON RECTUM
ALL 442 162
5P GAIN MUTATED 67 36
5P GAIN WILD-TYPE 375 126

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

'5p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0194 (Fisher's exact test), Q value = 0.14

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

nPatients N0 N1 N2
ALL 342 149 114
5P GAIN MUTATED 45 31 26
5P GAIN WILD-TYPE 297 118 88

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

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0232 (Fisher's exact test), Q value = 0.15

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

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
5P GAIN MUTATED 59 8 36 0
5P GAIN WILD-TYPE 322 52 110 13

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

'5p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0129 (Wilcoxon-test), Q value = 0.11

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

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
5P GAIN MUTATED 100 2.8 (4.3)
5P GAIN WILD-TYPE 473 2.1 (4.8)

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

'5q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0517 (Fisher's exact test), Q value = 0.25

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

nPatients COLON RECTUM
ALL 442 162
5Q GAIN MUTATED 40 24
5Q GAIN WILD-TYPE 402 138

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

'6p gain' versus 'NEOPLASM_DISEASESTAGE'

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

Table S23.  Gene #11: '6p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
6P GAIN MUTATED 18 0 3 24 2 1 6 7 21 15 15 9 1
6P GAIN WILD-TYPE 86 1 33 147 8 2 20 14 58 39 46 18 1

Figure S23.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'6p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00064 (Fisher's exact test), Q value = 0.015

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

nPatients N0 N1 N2
ALL 342 149 114
6P GAIN MUTATED 54 31 38
6P GAIN WILD-TYPE 288 118 76

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

'6p gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.000317 (Fisher's exact test), Q value = 0.011

Table S25.  Gene #11: '6p gain' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 9 599
6P GAIN MUTATED 7 117
6P GAIN WILD-TYPE 2 482

Figure S25.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'6p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000725 (Wilcoxon-test), Q value = 0.017

Table S26.  Gene #11: '6p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
6P GAIN MUTATED 120 3.3 (5.2)
6P GAIN WILD-TYPE 453 1.9 (4.6)

Figure S26.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'6q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0144 (Fisher's exact test), Q value = 0.12

Table S27.  Gene #12: '6q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
6Q GAIN MUTATED 16 0 3 20 2 0 6 6 18 13 13 11 1
6Q GAIN WILD-TYPE 88 1 33 151 8 3 20 15 61 41 48 16 1

Figure S27.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00213 (Fisher's exact test), Q value = 0.035

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

nPatients N0 N1 N2
ALL 342 149 114
6Q GAIN MUTATED 48 29 33
6Q GAIN WILD-TYPE 294 120 81

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

'6q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0135 (Fisher's exact test), Q value = 0.11

Table S29.  Gene #12: '6q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
6Q GAIN MUTATED 72 24
6Q GAIN WILD-TYPE 376 62

Figure S29.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'6q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00015 (Fisher's exact test), Q value = 0.0066

Table S30.  Gene #12: '6q gain' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 9 599
6Q GAIN MUTATED 7 104
6Q GAIN WILD-TYPE 2 495

Figure S30.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'6q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00256 (Wilcoxon-test), Q value = 0.038

Table S31.  Gene #12: '6q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
6Q GAIN MUTATED 107 3.1 (4.8)
6Q GAIN WILD-TYPE 466 2.0 (4.7)

Figure S31.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'7p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00017 (Fisher's exact test), Q value = 0.0072

Table S32.  Gene #13: '7p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
7P GAIN MUTATED 57 1 18 74 3 2 13 15 57 37 41 19 1
7P GAIN WILD-TYPE 47 0 18 97 7 1 13 6 22 17 20 8 1

Figure S32.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'7p gain' versus 'PATHOLOGY_N_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.0025

Table S33.  Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
7P GAIN MUTATED 167 102 75
7P GAIN WILD-TYPE 175 47 39

Figure S33.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0241 (Fisher's exact test), Q value = 0.16

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

nPatients 0 1
ALL 448 86
7P GAIN MUTATED 242 58
7P GAIN WILD-TYPE 206 28

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

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00037 (Fisher's exact test), Q value = 0.012

Table S35.  Gene #13: '7p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
7P GAIN MUTATED 218 25 98 3
7P GAIN WILD-TYPE 163 35 48 10

Figure S35.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 7.21e-05 (Wilcoxon-test), Q value = 0.0038

Table S36.  Gene #13: '7p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
7P GAIN MUTATED 330 2.6 (5.2)
7P GAIN WILD-TYPE 243 1.7 (4.0)

Figure S36.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'7q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00042 (Fisher's exact test), Q value = 0.012

Table S37.  Gene #14: '7q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
7Q GAIN MUTATED 54 1 16 63 3 1 12 10 53 32 37 18 1
7Q GAIN WILD-TYPE 50 0 20 108 7 2 14 11 26 22 24 9 1

Figure S37.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'7q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00139 (Fisher's exact test), Q value = 0.026

Table S38.  Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
7Q GAIN MUTATED 151 89 66
7Q GAIN WILD-TYPE 191 60 48

Figure S38.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'7q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00937 (Fisher's exact test), Q value = 0.093

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

nPatients 0 1
ALL 448 86
7Q GAIN MUTATED 211 54
7Q GAIN WILD-TYPE 237 32

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

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00487 (Fisher's exact test), Q value = 0.058

Table S40.  Gene #14: '7q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
7Q GAIN MUTATED 198 23 83 2
7Q GAIN WILD-TYPE 183 37 63 11

Figure S40.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00282 (Wilcoxon-test), Q value = 0.04

Table S41.  Gene #14: '7q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
7Q GAIN MUTATED 296 2.4 (4.7)
7Q GAIN WILD-TYPE 277 2.0 (4.7)

Figure S41.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'8p gain' versus 'COMPLETENESS_OF_RESECTION'

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

Table S42.  Gene #15: '8p gain' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 439 5 36 29
8P GAIN MUTATED 112 0 14 12
8P GAIN WILD-TYPE 327 5 22 17

Figure S42.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'8q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0464 (Fisher's exact test), Q value = 0.23

Table S43.  Gene #16: '8q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
8Q GAIN MUTATED 45 0 21 84 3 2 11 13 39 33 42 13 0
8Q GAIN WILD-TYPE 59 1 15 87 7 1 15 8 40 21 19 14 2

Figure S43.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'8q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0131 (Fisher's exact test), Q value = 0.11

Table S44.  Gene #16: '8q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
8Q GAIN MUTATED 219 55
8Q GAIN WILD-TYPE 229 31

Figure S44.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'8q gain' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0381 (Fisher's exact test), Q value = 0.2

Table S45.  Gene #16: '8q gain' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 9 599
8Q GAIN MUTATED 8 303
8Q GAIN WILD-TYPE 1 296

Figure S45.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'8q gain' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0265 (Fisher's exact test), Q value = 0.17

Table S46.  Gene #16: '8q gain' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 439 5 36 29
8Q GAIN MUTATED 212 3 26 17
8Q GAIN WILD-TYPE 227 2 10 12

Figure S46.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'9p gain' versus 'Time to Death'

P value = 0.00812 (logrank test), Q value = 0.083

Table S47.  Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 583 115 0.0 - 140.4 (19.1)
9P GAIN MUTATED 113 32 0.0 - 129.3 (16.2)
9P GAIN WILD-TYPE 470 83 0.0 - 140.4 (19.8)

Figure S47.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0384 (Fisher's exact test), Q value = 0.2

Table S48.  Gene #17: '9p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
9P GAIN MUTATED 79 42
9P GAIN WILD-TYPE 363 120

Figure S48.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'9p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0121 (Fisher's exact test), Q value = 0.11

Table S49.  Gene #17: '9p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
9P GAIN MUTATED 15 1 7 31 2 2 3 8 11 18 11 7 1
9P GAIN WILD-TYPE 89 0 29 140 8 1 23 13 68 36 50 20 1

Figure S49.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00545 (Fisher's exact test), Q value = 0.062

Table S50.  Gene #17: '9p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
9P GAIN MUTATED 61 18 36 5
9P GAIN WILD-TYPE 320 42 110 8

Figure S50.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'9q gain' versus 'Time to Death'

P value = 0.00626 (logrank test), Q value = 0.068

Table S51.  Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 583 115 0.0 - 140.4 (19.1)
9Q GAIN MUTATED 94 28 0.0 - 129.3 (15.0)
9Q GAIN WILD-TYPE 489 87 0.0 - 140.4 (20.0)

Figure S51.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

'9q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0493 (Fisher's exact test), Q value = 0.24

Table S52.  Gene #18: '9q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
9Q GAIN MUTATED 13 1 5 29 1 2 3 6 8 14 11 4 1
9Q GAIN WILD-TYPE 91 0 31 142 9 1 23 15 71 40 50 23 1

Figure S52.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0287 (Fisher's exact test), Q value = 0.17

Table S53.  Gene #18: '9q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
9Q GAIN MUTATED 53 16 27 4
9Q GAIN WILD-TYPE 328 44 119 9

Figure S53.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'Time to Death'

P value = 0.0412 (logrank test), Q value = 0.21

Table S54.  Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 583 115 0.0 - 140.4 (19.1)
10P GAIN MUTATED 43 13 0.0 - 91.8 (16.3)
10P GAIN WILD-TYPE 540 102 0.0 - 140.4 (19.2)

Figure S54.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #1: 'Time to Death'

'10p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0306 (Fisher's exact test), Q value = 0.18

Table S55.  Gene #19: '10p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
10P GAIN MUTATED 22 9 16
10P GAIN WILD-TYPE 320 140 98

Figure S55.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'10q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0383 (Wilcoxon-test), Q value = 0.2

Table S56.  Gene #20: '10q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
10Q GAIN MUTATED 25 3.9 (5.3)
10Q GAIN WILD-TYPE 548 2.2 (4.7)

Figure S56.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'10q gain' versus 'RACE'

P value = 0.038 (Fisher's exact test), Q value = 0.2

Table S57.  Gene #20: '10q gain' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 12 60 292
10Q GAIN MUTATED 1 1 4 13
10Q GAIN WILD-TYPE 0 11 56 279

Figure S57.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #13: 'RACE'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00572 (Wilcoxon-test), Q value = 0.063

Table S58.  Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 606 66.3 (12.7)
11P GAIN MUTATED 84 62.8 (12.4)
11P GAIN WILD-TYPE 522 66.8 (12.7)

Figure S58.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0234 (Fisher's exact test), Q value = 0.15

Table S59.  Gene #21: '11p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
11P GAIN MUTATED 52 31
11P GAIN WILD-TYPE 390 131

Figure S59.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00198 (Fisher's exact test), Q value = 0.034

Table S60.  Gene #21: '11p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
11P GAIN MUTATED 50 2 31 0
11P GAIN WILD-TYPE 331 58 115 13

Figure S60.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 5.62e-05 (Wilcoxon-test), Q value = 0.0032

Table S61.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 606 66.3 (12.7)
11Q GAIN MUTATED 76 60.8 (12.2)
11Q GAIN WILD-TYPE 530 67.1 (12.6)

Figure S61.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00353 (Fisher's exact test), Q value = 0.046

Table S62.  Gene #22: '11q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
11Q GAIN MUTATED 49 1 26 0
11Q GAIN WILD-TYPE 332 59 120 13

Figure S62.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0396 (Wilcoxon-test), Q value = 0.2

Table S63.  Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 606 66.3 (12.7)
12Q GAIN MUTATED 111 68.5 (12.3)
12Q GAIN WILD-TYPE 495 65.8 (12.8)

Figure S63.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0289 (Fisher's exact test), Q value = 0.17

Table S64.  Gene #24: '12q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
12Q GAIN MUTATED 16 1 9 45 1 0 3 6 9 8 6 7 0
12Q GAIN WILD-TYPE 88 0 27 126 9 3 23 15 70 46 55 20 2

Figure S64.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00947 (Fisher's exact test), Q value = 0.093

Table S65.  Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
12Q GAIN MUTATED 75 25 11
12Q GAIN WILD-TYPE 267 124 103

Figure S65.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0049 (Wilcoxon-test), Q value = 0.058

Table S66.  Gene #24: '12q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
12Q GAIN MUTATED 107 1.1 (2.0)
12Q GAIN WILD-TYPE 466 2.5 (5.1)

Figure S66.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'13q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0149 (Fisher's exact test), Q value = 0.12

Table S67.  Gene #25: '13q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
13Q GAIN MUTATED 251 110
13Q GAIN WILD-TYPE 191 52

Figure S67.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'13q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00101 (Fisher's exact test), Q value = 0.02

Table S68.  Gene #25: '13q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
13Q GAIN MUTATED 60 0 18 86 4 3 15 17 53 37 47 17 0
13Q GAIN WILD-TYPE 44 1 18 85 6 0 11 4 26 17 14 10 2

Figure S68.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'13q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00026 (Fisher's exact test), Q value = 0.0098

Table S69.  Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
13Q GAIN MUTATED 181 103 79
13Q GAIN WILD-TYPE 161 46 35

Figure S69.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'13q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0304 (Fisher's exact test), Q value = 0.18

Table S70.  Gene #25: '13q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
13Q GAIN MUTATED 261 61
13Q GAIN WILD-TYPE 187 25

Figure S70.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00081

Table S71.  Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
13Q GAIN MUTATED 234 17 106 3
13Q GAIN WILD-TYPE 147 43 40 10

Figure S71.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'13q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00112 (Wilcoxon-test), Q value = 0.022

Table S72.  Gene #25: '13q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
13Q GAIN MUTATED 350 2.4 (4.1)
13Q GAIN WILD-TYPE 223 2.0 (5.5)

Figure S72.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'14q gain' versus 'RACE'

P value = 0.0277 (Fisher's exact test), Q value = 0.17

Table S73.  Gene #26: '14q gain' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 12 60 292
14Q GAIN MUTATED 1 2 2 22
14Q GAIN WILD-TYPE 0 10 58 270

Figure S73.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #13: 'RACE'

'16p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0177 (Fisher's exact test), Q value = 0.13

Table S74.  Gene #28: '16p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
16P GAIN MUTATED 18 1 4 32 3 0 7 9 25 18 17 6 1
16P GAIN WILD-TYPE 86 0 32 139 7 3 19 12 54 36 44 21 1

Figure S74.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'16p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00239 (Fisher's exact test), Q value = 0.037

Table S75.  Gene #28: '16p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
16P GAIN MUTATED 64 46 35
16P GAIN WILD-TYPE 278 103 79

Figure S75.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00326 (Fisher's exact test), Q value = 0.043

Table S76.  Gene #28: '16p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
16P GAIN MUTATED 99 6 40 0
16P GAIN WILD-TYPE 282 54 106 13

Figure S76.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00324 (Wilcoxon-test), Q value = 0.043

Table S77.  Gene #28: '16p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
16P GAIN MUTATED 138 2.5 (3.7)
16P GAIN WILD-TYPE 435 2.1 (5.0)

Figure S77.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'16q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00551 (Fisher's exact test), Q value = 0.062

Table S78.  Gene #29: '16q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
16Q GAIN MUTATED 17 1 4 31 2 0 7 10 27 16 16 7 1
16Q GAIN WILD-TYPE 87 0 32 140 8 3 19 11 52 38 45 20 1

Figure S78.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'16q gain' versus 'PATHOLOGY_N_STAGE'

P value = 5e-04 (Fisher's exact test), Q value = 0.013

Table S79.  Gene #29: '16q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
16Q GAIN MUTATED 61 48 34
16Q GAIN WILD-TYPE 281 101 80

Figure S79.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00326 (Fisher's exact test), Q value = 0.043

Table S80.  Gene #29: '16q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
16Q GAIN MUTATED 96 6 41 0
16Q GAIN WILD-TYPE 285 54 105 13

Figure S80.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00206 (Wilcoxon-test), Q value = 0.034

Table S81.  Gene #29: '16q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
16Q GAIN MUTATED 137 2.5 (3.8)
16Q GAIN WILD-TYPE 436 2.1 (5.0)

Figure S81.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'17p gain' versus 'Time to Death'

P value = 0.037 (logrank test), Q value = 0.2

Table S82.  Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 583 115 0.0 - 140.4 (19.1)
17P GAIN MUTATED 38 2 0.1 - 102.4 (18.5)
17P GAIN WILD-TYPE 545 113 0.0 - 140.4 (19.1)

Figure S82.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'RACE'

P value = 0.0386 (Fisher's exact test), Q value = 0.2

Table S83.  Gene #30: '17p gain' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 12 60 292
17P GAIN MUTATED 1 1 6 17
17P GAIN WILD-TYPE 0 11 54 275

Figure S83.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #13: 'RACE'

'17q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0183 (Fisher's exact test), Q value = 0.14

Table S84.  Gene #31: '17q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
17Q GAIN MUTATED 69 23
17Q GAIN WILD-TYPE 379 63

Figure S84.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'18p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0171 (Fisher's exact test), Q value = 0.13

Table S85.  Gene #32: '18p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
18P GAIN MUTATED 5 0 5 4 0 0 3 1 3 7 4 0 1
18P GAIN WILD-TYPE 99 1 31 167 10 3 23 20 76 47 57 27 1

Figure S85.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'18p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0147 (Fisher's exact test), Q value = 0.12

Table S86.  Gene #32: '18p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
18P GAIN MUTATED 14 6 13
18P GAIN WILD-TYPE 328 143 101

Figure S86.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0446 (Fisher's exact test), Q value = 0.22

Table S87.  Gene #32: '18p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
18P GAIN MUTATED 18 7 6 2
18P GAIN WILD-TYPE 363 53 140 11

Figure S87.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0134 (Wilcoxon-test), Q value = 0.11

Table S88.  Gene #32: '18p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
18P GAIN MUTATED 31 4.6 (6.8)
18P GAIN WILD-TYPE 542 2.1 (4.5)

Figure S88.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'20p gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0201 (Fisher's exact test), Q value = 0.14

Table S89.  Gene #36: '20p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
20P GAIN MUTATED 241 106
20P GAIN WILD-TYPE 201 56

Figure S89.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'20p gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00041 (Fisher's exact test), Q value = 0.012

Table S90.  Gene #36: '20p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
20P GAIN MUTATED 63 1 13 86 4 2 13 18 41 32 47 18 1
20P GAIN WILD-TYPE 41 0 23 85 6 1 13 3 38 22 14 9 1

Figure S90.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'20p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.046 (Fisher's exact test), Q value = 0.23

Table S91.  Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
20P GAIN MUTATED 181 91 74
20P GAIN WILD-TYPE 161 58 40

Figure S91.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'20p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.000785 (Fisher's exact test), Q value = 0.018

Table S92.  Gene #36: '20p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
20P GAIN MUTATED 246 64
20P GAIN WILD-TYPE 202 22

Figure S92.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00081

Table S93.  Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
20P GAIN MUTATED 220 20 100 4
20P GAIN WILD-TYPE 161 40 46 9

Figure S93.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0265 (Wilcoxon-test), Q value = 0.17

Table S94.  Gene #36: '20p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
20P GAIN MUTATED 333 2.4 (4.8)
20P GAIN WILD-TYPE 240 2.0 (4.6)

Figure S94.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'20q gain' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 1.3e-06 (Fisher's exact test), Q value = 0.00046

Table S95.  Gene #37: '20q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
20Q GAIN MUTATED 312 144
20Q GAIN WILD-TYPE 130 18

Figure S95.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'20q gain' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00028 (Fisher's exact test), Q value = 0.0099

Table S96.  Gene #37: '20q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
20Q GAIN MUTATED 79 1 21 115 5 3 18 20 62 44 55 24 1
20Q GAIN WILD-TYPE 25 0 15 56 5 0 8 1 17 10 6 3 1

Figure S96.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00042 (Fisher's exact test), Q value = 0.012

Table S97.  Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
20Q GAIN MUTATED 238 127 91
20Q GAIN WILD-TYPE 104 22 23

Figure S97.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'20q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.000868 (Fisher's exact test), Q value = 0.019

Table S98.  Gene #37: '20q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
20Q GAIN MUTATED 327 77
20Q GAIN WILD-TYPE 121 9

Figure S98.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00081

Table S99.  Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
20Q GAIN MUTATED 286 25 135 7
20Q GAIN WILD-TYPE 95 35 11 6

Figure S99.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0176 (Fisher's exact test), Q value = 0.13

Table S100.  Gene #37: '20q gain' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 439 5 36 29
20Q GAIN MUTATED 330 4 32 16
20Q GAIN WILD-TYPE 109 1 4 13

Figure S100.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'20q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0023 (Wilcoxon-test), Q value = 0.037

Table S101.  Gene #37: '20q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
20Q GAIN MUTATED 436 2.4 (4.7)
20Q GAIN WILD-TYPE 137 1.8 (4.7)

Figure S101.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0189 (Wilcoxon-test), Q value = 0.14

Table S102.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 606 66.3 (12.7)
21Q GAIN MUTATED 34 61.9 (11.3)
21Q GAIN WILD-TYPE 572 66.5 (12.8)

Figure S102.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00435 (Fisher's exact test), Q value = 0.053

Table S103.  Gene #42: '1p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
1P LOSS MUTATED 60 38 36
1P LOSS WILD-TYPE 282 111 78

Figure S103.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'1p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.016 (Fisher's exact test), Q value = 0.12

Table S104.  Gene #42: '1p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
1P LOSS MUTATED 91 28
1P LOSS WILD-TYPE 357 58

Figure S104.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'1p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0106 (Fisher's exact test), Q value = 0.1

Table S105.  Gene #42: '1p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
1P LOSS MUTATED 81 9 44 0
1P LOSS WILD-TYPE 300 51 102 13

Figure S105.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000658 (Wilcoxon-test), Q value = 0.015

Table S106.  Gene #42: '1p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
1P LOSS MUTATED 126 3.5 (6.3)
1P LOSS WILD-TYPE 447 1.9 (4.1)

Figure S106.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'1q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.029 (Fisher's exact test), Q value = 0.17

Table S107.  Gene #43: '1q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
1Q LOSS MUTATED 48 17
1Q LOSS WILD-TYPE 400 69

Figure S107.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'2p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00101 (Fisher's exact test), Q value = 0.02

Table S108.  Gene #44: '2p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
2P LOSS MUTATED 6 11
2P LOSS WILD-TYPE 436 151

Figure S108.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'2p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0101 (Fisher's exact test), Q value = 0.098

Table S109.  Gene #44: '2p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
2P LOSS MUTATED 6 0 9 1
2P LOSS WILD-TYPE 375 60 137 12

Figure S109.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0321 (Fisher's exact test), Q value = 0.18

Table S110.  Gene #46: '3p loss' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 20 107 413 66
3P LOSS MUTATED 2 4 52 9
3P LOSS WILD-TYPE 18 103 361 57

Figure S110.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #5: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0319 (Fisher's exact test), Q value = 0.18

Table S111.  Gene #46: '3p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
3P LOSS MUTATED 28 21 18
3P LOSS WILD-TYPE 314 128 96

Figure S111.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'3p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.004 (Fisher's exact test), Q value = 0.05

Table S112.  Gene #46: '3p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
3P LOSS MUTATED 41 18
3P LOSS WILD-TYPE 407 68

Figure S112.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'3p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0225 (Wilcoxon-test), Q value = 0.15

Table S113.  Gene #46: '3p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
3P LOSS MUTATED 62 3.3 (5.6)
3P LOSS WILD-TYPE 511 2.1 (4.6)

Figure S113.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'3q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0333 (Fisher's exact test), Q value = 0.19

Table S114.  Gene #47: '3q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
3Q LOSS MUTATED 26 11
3Q LOSS WILD-TYPE 422 75

Figure S114.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'3q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00732 (Fisher's exact test), Q value = 0.077

Table S115.  Gene #47: '3q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
3Q LOSS MUTATED 30 3 5 4
3Q LOSS WILD-TYPE 351 57 141 9

Figure S115.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0248 (Fisher's exact test), Q value = 0.16

Table S116.  Gene #48: '4p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
4P LOSS MUTATED 26 0 6 49 2 0 7 9 25 22 30 11 1
4P LOSS WILD-TYPE 78 1 30 122 8 3 19 12 54 32 31 16 1

Figure S116.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00113 (Fisher's exact test), Q value = 0.022

Table S117.  Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
4P LOSS MUTATED 88 56 48
4P LOSS WILD-TYPE 254 93 66

Figure S117.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000554 (Fisher's exact test), Q value = 0.014

Table S118.  Gene #48: '4p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
4P LOSS MUTATED 126 41
4P LOSS WILD-TYPE 322 45

Figure S118.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0294 (Fisher's exact test), Q value = 0.18

Table S119.  Gene #48: '4p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
4P LOSS MUTATED 122 10 54 3
4P LOSS WILD-TYPE 259 50 92 10

Figure S119.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.000585 (Fisher's exact test), Q value = 0.015

Table S120.  Gene #48: '4p loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 9 599
4P LOSS MUTATED 8 184
4P LOSS WILD-TYPE 1 415

Figure S120.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'4p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000481 (Wilcoxon-test), Q value = 0.013

Table S121.  Gene #48: '4p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
4P LOSS MUTATED 183 3.0 (5.1)
4P LOSS WILD-TYPE 390 1.8 (4.5)

Figure S121.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'4q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00901 (Fisher's exact test), Q value = 0.09

Table S122.  Gene #49: '4q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
4Q LOSS MUTATED 119 62
4Q LOSS WILD-TYPE 323 100

Figure S122.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0023 (Fisher's exact test), Q value = 0.037

Table S123.  Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
4Q LOSS MUTATED 85 56 44
4Q LOSS WILD-TYPE 257 93 70

Figure S123.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0109 (Fisher's exact test), Q value = 0.1

Table S124.  Gene #49: '4q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
4Q LOSS MUTATED 108 11 58 3
4Q LOSS WILD-TYPE 273 49 88 10

Figure S124.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.000438 (Fisher's exact test), Q value = 0.012

Table S125.  Gene #49: '4q loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 9 599
4Q LOSS MUTATED 8 177
4Q LOSS WILD-TYPE 1 422

Figure S125.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'4q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00158 (Wilcoxon-test), Q value = 0.029

Table S126.  Gene #49: '4q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
4Q LOSS MUTATED 175 3.0 (5.1)
4Q LOSS WILD-TYPE 398 1.9 (4.5)

Figure S126.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'5p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0172 (Fisher's exact test), Q value = 0.13

Table S127.  Gene #50: '5p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
5P LOSS MUTATED 15 0 4 14 0 2 4 6 11 11 7 8 0
5P LOSS WILD-TYPE 89 1 32 157 10 1 22 15 68 43 54 19 2

Figure S127.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'5p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0397 (Fisher's exact test), Q value = 0.2

Table S128.  Gene #50: '5p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
5P LOSS MUTATED 37 27 20
5P LOSS WILD-TYPE 305 122 94

Figure S128.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'5p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0247 (Fisher's exact test), Q value = 0.16

Table S129.  Gene #50: '5p loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 9 599
5P LOSS MUTATED 4 80
5P LOSS WILD-TYPE 5 519

Figure S129.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'5p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0296 (Wilcoxon-test), Q value = 0.18

Table S130.  Gene #50: '5p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
5P LOSS MUTATED 80 3.7 (7.1)
5P LOSS WILD-TYPE 493 2.0 (4.1)

Figure S130.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'5q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0384 (Fisher's exact test), Q value = 0.2

Table S131.  Gene #51: '5q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
5Q LOSS MUTATED 78 41
5Q LOSS WILD-TYPE 364 121

Figure S131.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0115 (Fisher's exact test), Q value = 0.1

Table S132.  Gene #51: '5q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
5Q LOSS MUTATED 55 31 33
5Q LOSS WILD-TYPE 287 118 81

Figure S132.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0528 (Fisher's exact test), Q value = 0.25

Table S133.  Gene #51: '5q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
5Q LOSS MUTATED 79 23
5Q LOSS WILD-TYPE 369 63

Figure S133.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0436 (Fisher's exact test), Q value = 0.22

Table S134.  Gene #51: '5q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
5Q LOSS MUTATED 71 7 39 1
5Q LOSS WILD-TYPE 310 53 107 12

Figure S134.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00252 (Fisher's exact test), Q value = 0.038

Table S135.  Gene #51: '5q loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 9 599
5Q LOSS MUTATED 6 113
5Q LOSS WILD-TYPE 3 486

Figure S135.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'5q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00587 (Wilcoxon-test), Q value = 0.064

Table S136.  Gene #51: '5q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
5Q LOSS MUTATED 114 3.2 (5.6)
5Q LOSS WILD-TYPE 459 2.0 (4.4)

Figure S136.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'6p loss' versus 'Time to Death'

P value = 0.0126 (logrank test), Q value = 0.11

Table S137.  Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 583 115 0.0 - 140.4 (19.1)
6P LOSS MUTATED 42 12 2.0 - 45.4 (16.8)
6P LOSS WILD-TYPE 541 103 0.0 - 140.4 (19.3)

Figure S137.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0522 (Fisher's exact test), Q value = 0.25

Table S138.  Gene #52: '6p loss' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 439 5 36 29
6P LOSS MUTATED 31 0 1 6
6P LOSS WILD-TYPE 408 5 35 23

Figure S138.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'6p loss' versus 'RACE'

P value = 0.00514 (Fisher's exact test), Q value = 0.059

Table S139.  Gene #52: '6p loss' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 12 60 292
6P LOSS MUTATED 0 4 1 23
6P LOSS WILD-TYPE 1 8 59 269

Figure S139.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #13: 'RACE'

'6q loss' versus 'Time to Death'

P value = 0.0205 (logrank test), Q value = 0.14

Table S140.  Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 583 115 0.0 - 140.4 (19.1)
6Q LOSS MUTATED 64 16 0.5 - 61.0 (14.6)
6Q LOSS WILD-TYPE 519 99 0.0 - 140.4 (20.0)

Figure S140.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0392 (Fisher's exact test), Q value = 0.2

Table S141.  Gene #53: '6q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
6Q LOSS MUTATED 38 7 16 5
6Q LOSS WILD-TYPE 343 53 130 8

Figure S141.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0534 (Wilcoxon-test), Q value = 0.25

Table S142.  Gene #53: '6q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
6Q LOSS MUTATED 62 3.6 (6.4)
6Q LOSS WILD-TYPE 511 2.1 (4.4)

Figure S142.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'6q loss' versus 'RACE'

P value = 0.00449 (Fisher's exact test), Q value = 0.054

Table S143.  Gene #53: '6q loss' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 12 60 292
6Q LOSS MUTATED 1 4 3 29
6Q LOSS WILD-TYPE 0 8 57 263

Figure S143.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #13: 'RACE'

'8p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00284 (Fisher's exact test), Q value = 0.04

Table S144.  Gene #55: '8p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
8P LOSS MUTATED 140 73
8P LOSS WILD-TYPE 302 89

Figure S144.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'8p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.04 (Fisher's exact test), Q value = 0.21

Table S145.  Gene #55: '8p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
8P LOSS MUTATED 29 0 9 51 2 1 12 10 28 24 31 12 1
8P LOSS WILD-TYPE 75 1 27 120 8 2 14 11 51 30 30 15 1

Figure S145.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'8p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00049 (Fisher's exact test), Q value = 0.013

Table S146.  Gene #55: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
8P LOSS MUTATED 99 61 54
8P LOSS WILD-TYPE 243 88 60

Figure S146.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'8p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00664 (Fisher's exact test), Q value = 0.071

Table S147.  Gene #55: '8p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
8P LOSS MUTATED 148 42
8P LOSS WILD-TYPE 300 44

Figure S147.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00255 (Fisher's exact test), Q value = 0.038

Table S148.  Gene #55: '8p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
8P LOSS MUTATED 127 12 67 5
8P LOSS WILD-TYPE 254 48 79 8

Figure S148.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00011 (Wilcoxon-test), Q value = 0.005

Table S149.  Gene #55: '8p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
8P LOSS MUTATED 206 3.2 (6.2)
8P LOSS WILD-TYPE 367 1.7 (3.5)

Figure S149.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'8q loss' versus 'GENDER'

P value = 0.024 (Fisher's exact test), Q value = 0.16

Table S150.  Gene #56: '8q loss' versus Clinical Feature #8: 'GENDER'

nPatients FEMALE MALE
ALL 286 322
8Q LOSS MUTATED 10 26
8Q LOSS WILD-TYPE 276 296

Figure S150.  Get High-res Image Gene #56: '8q loss' versus Clinical Feature #8: 'GENDER'

'9p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.05 (Fisher's exact test), Q value = 0.24

Table S151.  Gene #57: '9p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
9P LOSS MUTATED 51 17
9P LOSS WILD-TYPE 397 69

Figure S151.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'9p loss' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0459 (Fisher's exact test), Q value = 0.23

Table S152.  Gene #57: '9p loss' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 439 5 36 29
9P LOSS MUTATED 47 2 8 3
9P LOSS WILD-TYPE 392 3 28 26

Figure S152.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'9q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0314 (Wilcoxon-test), Q value = 0.18

Table S153.  Gene #58: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 606 66.3 (12.7)
9Q LOSS MUTATED 75 63.7 (11.3)
9Q LOSS WILD-TYPE 531 66.6 (12.9)

Figure S153.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0203 (Fisher's exact test), Q value = 0.14

Table S154.  Gene #58: '9q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
9Q LOSS MUTATED 50 18
9Q LOSS WILD-TYPE 398 68

Figure S154.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00519 (Wilcoxon-test), Q value = 0.059

Table S155.  Gene #59: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 606 66.3 (12.7)
10P LOSS MUTATED 100 62.9 (13.2)
10P LOSS WILD-TYPE 506 66.9 (12.5)

Figure S155.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0227 (Fisher's exact test), Q value = 0.15

Table S156.  Gene #59: '10p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
10P LOSS MUTATED 60 6 27 6
10P LOSS WILD-TYPE 321 54 119 7

Figure S156.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00795 (Fisher's exact test), Q value = 0.082

Table S157.  Gene #59: '10p loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 9 599
10P LOSS MUTATED 5 95
10P LOSS WILD-TYPE 4 504

Figure S157.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'10p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0195 (Wilcoxon-test), Q value = 0.14

Table S158.  Gene #59: '10p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
10P LOSS MUTATED 95 2.7 (4.5)
10P LOSS WILD-TYPE 478 2.1 (4.7)

Figure S158.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0214 (Wilcoxon-test), Q value = 0.15

Table S159.  Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 606 66.3 (12.7)
10Q LOSS MUTATED 110 63.7 (12.8)
10Q LOSS WILD-TYPE 496 66.8 (12.7)

Figure S159.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0191 (Fisher's exact test), Q value = 0.14

Table S160.  Gene #60: '10q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
10Q LOSS MUTATED 66 6 31 6
10Q LOSS WILD-TYPE 315 54 115 7

Figure S160.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0121 (Fisher's exact test), Q value = 0.11

Table S161.  Gene #60: '10q loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 9 599
10Q LOSS MUTATED 5 105
10Q LOSS WILD-TYPE 4 494

Figure S161.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'11p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0116 (Fisher's exact test), Q value = 0.1

Table S162.  Gene #61: '11p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
11P LOSS MUTATED 30 24 20
11P LOSS WILD-TYPE 312 125 94

Figure S162.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'11p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000418 (Wilcoxon-test), Q value = 0.012

Table S163.  Gene #61: '11p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
11P LOSS MUTATED 70 3.8 (6.0)
11P LOSS WILD-TYPE 503 2.0 (4.5)

Figure S163.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'12p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.046 (Fisher's exact test), Q value = 0.23

Table S164.  Gene #63: '12p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
12P LOSS MUTATED 30 23 17
12P LOSS WILD-TYPE 312 126 97

Figure S164.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.011 (Fisher's exact test), Q value = 0.1

Table S165.  Gene #63: '12p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
12P LOSS MUTATED 45 1 23 0
12P LOSS WILD-TYPE 336 59 123 13

Figure S165.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0469 (Wilcoxon-test), Q value = 0.23

Table S166.  Gene #63: '12p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
12P LOSS MUTATED 68 2.5 (4.0)
12P LOSS WILD-TYPE 505 2.2 (4.8)

Figure S166.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'12q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0229 (Fisher's exact test), Q value = 0.15

Table S167.  Gene #64: '12q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
12Q LOSS MUTATED 29 23 18
12Q LOSS WILD-TYPE 313 126 96

Figure S167.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'12q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0114 (Wilcoxon-test), Q value = 0.1

Table S168.  Gene #64: '12q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
12Q LOSS MUTATED 67 3.0 (5.0)
12Q LOSS WILD-TYPE 506 2.1 (4.7)

Figure S168.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0344 (Fisher's exact test), Q value = 0.19

Table S169.  Gene #65: '13q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
13Q LOSS MUTATED 8 3 6 2
13Q LOSS WILD-TYPE 373 57 140 11

Figure S169.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'13q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00702 (Wilcoxon-test), Q value = 0.075

Table S170.  Gene #65: '13q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
13Q LOSS MUTATED 17 8.4 (13.3)
13Q LOSS WILD-TYPE 556 2.0 (4.1)

Figure S170.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'RACE'

P value = 0.0168 (Fisher's exact test), Q value = 0.13

Table S171.  Gene #65: '13q loss' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 12 60 292
13Q LOSS MUTATED 1 1 1 7
13Q LOSS WILD-TYPE 0 11 59 285

Figure S171.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #13: 'RACE'

'14q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0191 (Fisher's exact test), Q value = 0.14

Table S172.  Gene #66: '14q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
14Q LOSS MUTATED 134 66
14Q LOSS WILD-TYPE 308 96

Figure S172.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'14q loss' versus 'PATHOLOGY_N_STAGE'

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

Table S173.  Gene #66: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
14Q LOSS MUTATED 103 63 36
14Q LOSS WILD-TYPE 239 86 78

Figure S173.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'14q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0342 (Fisher's exact test), Q value = 0.19

Table S174.  Gene #66: '14q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
14Q LOSS MUTATED 143 38
14Q LOSS WILD-TYPE 305 48

Figure S174.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00081

Table S175.  Gene #66: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
14Q LOSS MUTATED 129 4 64 1
14Q LOSS WILD-TYPE 252 56 82 12

Figure S175.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0317 (Fisher's exact test), Q value = 0.18

Table S176.  Gene #67: '15q loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
15Q LOSS MUTATED 33 0 7 57 3 2 7 11 30 26 31 12 1
15Q LOSS WILD-TYPE 71 1 29 114 7 1 19 10 49 28 30 15 1

Figure S176.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00888 (Fisher's exact test), Q value = 0.09

Table S177.  Gene #67: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
15Q LOSS MUTATED 109 66 50
15Q LOSS WILD-TYPE 233 83 64

Figure S177.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0101 (Fisher's exact test), Q value = 0.098

Table S178.  Gene #67: '15q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
15Q LOSS MUTATED 155 43
15Q LOSS WILD-TYPE 293 43

Figure S178.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0116 (Fisher's exact test), Q value = 0.1

Table S179.  Gene #67: '15q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
15Q LOSS MUTATED 139 12 64 5
15Q LOSS WILD-TYPE 242 48 82 8

Figure S179.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0151 (Fisher's exact test), Q value = 0.12

Table S180.  Gene #67: '15q loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 9 599
15Q LOSS MUTATED 7 218
15Q LOSS WILD-TYPE 2 381

Figure S180.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'15q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00272 (Wilcoxon-test), Q value = 0.04

Table S181.  Gene #67: '15q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
15Q LOSS MUTATED 211 2.8 (5.0)
15Q LOSS WILD-TYPE 362 1.9 (4.5)

Figure S181.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'17p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.0164 (Fisher's exact test), Q value = 0.13

Table S182.  Gene #70: '17p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
17P LOSS MUTATED 229 102
17P LOSS WILD-TYPE 213 60

Figure S182.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'17p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0051 (Fisher's exact test), Q value = 0.059

Table S183.  Gene #70: '17p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
17P LOSS MUTATED 46 0 18 84 3 2 14 15 45 37 43 18 2
17P LOSS WILD-TYPE 58 1 18 87 7 1 12 6 34 17 18 9 0

Figure S183.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00127 (Fisher's exact test), Q value = 0.024

Table S184.  Gene #70: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
17P LOSS MUTATED 166 93 74
17P LOSS WILD-TYPE 176 56 40

Figure S184.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00197 (Fisher's exact test), Q value = 0.034

Table S185.  Gene #70: '17p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
17P LOSS MUTATED 236 61
17P LOSS WILD-TYPE 212 25

Figure S185.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00081

Table S186.  Gene #70: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
17P LOSS MUTATED 213 15 95 6
17P LOSS WILD-TYPE 168 45 51 7

Figure S186.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000281 (Wilcoxon-test), Q value = 0.0099

Table S187.  Gene #70: '17p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
17P LOSS MUTATED 316 2.7 (5.3)
17P LOSS WILD-TYPE 257 1.7 (3.8)

Figure S187.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'17q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0108 (Fisher's exact test), Q value = 0.1

Table S188.  Gene #71: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
17Q LOSS MUTATED 41 32 23
17Q LOSS WILD-TYPE 301 117 91

Figure S188.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'17q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000845 (Wilcoxon-test), Q value = 0.019

Table S189.  Gene #71: '17q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
17Q LOSS MUTATED 89 3.5 (6.7)
17Q LOSS WILD-TYPE 484 2.0 (4.2)

Figure S189.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0264 (Wilcoxon-test), Q value = 0.17

Table S190.  Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 606 66.3 (12.7)
18P LOSS MUTATED 374 65.6 (12.0)
18P LOSS WILD-TYPE 232 67.4 (13.8)

Figure S190.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 4.65e-07 (Fisher's exact test), Q value = 0.00024

Table S191.  Gene #72: '18p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
18P LOSS MUTATED 245 126
18P LOSS WILD-TYPE 197 36

Figure S191.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'18p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.0048

Table S192.  Gene #72: '18p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
18P LOSS MUTATED 57 0 16 97 4 3 11 14 54 37 49 23 1
18P LOSS WILD-TYPE 47 1 20 74 6 0 15 7 25 17 12 4 1

Figure S192.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'18p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.003 (Fisher's exact test), Q value = 0.042

Table S193.  Gene #72: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
18P LOSS MUTATED 190 104 78
18P LOSS WILD-TYPE 152 45 36

Figure S193.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'18p loss' versus 'PATHOLOGY_M_STAGE'

P value = 4.99e-06 (Fisher's exact test), Q value = 0.00081

Table S194.  Gene #72: '18p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
18P LOSS MUTATED 261 72
18P LOSS WILD-TYPE 187 14

Figure S194.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00081

Table S195.  Gene #72: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
18P LOSS MUTATED 232 12 119 7
18P LOSS WILD-TYPE 149 48 27 6

Figure S195.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0236 (Fisher's exact test), Q value = 0.16

Table S196.  Gene #72: '18p loss' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 439 5 36 29
18P LOSS MUTATED 266 2 29 14
18P LOSS WILD-TYPE 173 3 7 15

Figure S196.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'18p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00191 (Wilcoxon-test), Q value = 0.034

Table S197.  Gene #72: '18p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
18P LOSS MUTATED 352 2.5 (4.9)
18P LOSS WILD-TYPE 221 1.9 (4.4)

Figure S197.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0158 (Wilcoxon-test), Q value = 0.12

Table S198.  Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 606 66.3 (12.7)
18Q LOSS MUTATED 404 65.6 (12.1)
18Q LOSS WILD-TYPE 202 67.7 (13.8)

Figure S198.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 3.52e-09 (Fisher's exact test), Q value = 3.7e-06

Table S199.  Gene #73: '18q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
18Q LOSS MUTATED 264 137
18Q LOSS WILD-TYPE 178 25

Figure S199.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'18q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.002

Table S200.  Gene #73: '18q loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
18Q LOSS MUTATED 58 0 20 104 4 3 13 16 58 42 52 24 1
18Q LOSS WILD-TYPE 46 1 16 67 6 0 13 5 21 12 9 3 1

Figure S200.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.002

Table S201.  Gene #73: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
18Q LOSS MUTATED 201 112 88
18Q LOSS WILD-TYPE 141 37 26

Figure S201.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'18q loss' versus 'PATHOLOGY_M_STAGE'

P value = 8.27e-06 (Fisher's exact test), Q value = 0.00081

Table S202.  Gene #73: '18q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
18Q LOSS MUTATED 285 75
18Q LOSS WILD-TYPE 163 11

Figure S202.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00081

Table S203.  Gene #73: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
18Q LOSS MUTATED 248 15 126 10
18Q LOSS WILD-TYPE 133 45 20 3

Figure S203.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18q loss' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0222 (Fisher's exact test), Q value = 0.15

Table S204.  Gene #73: '18q loss' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 439 5 36 29
18Q LOSS MUTATED 289 3 30 14
18Q LOSS WILD-TYPE 150 2 6 15

Figure S204.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #11: 'COMPLETENESS_OF_RESECTION'

'18q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 5.81e-05 (Wilcoxon-test), Q value = 0.0032

Table S205.  Gene #73: '18q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
18Q LOSS MUTATED 382 2.5 (5.0)
18Q LOSS WILD-TYPE 191 1.6 (4.0)

Figure S205.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'19p loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00296 (Fisher's exact test), Q value = 0.042

Table S206.  Gene #74: '19p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
19P LOSS MUTATED 8 0 2 10 1 2 4 2 6 9 10 7 1
19P LOSS WILD-TYPE 96 1 34 161 9 1 22 19 73 45 51 20 1

Figure S206.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'19p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00026 (Fisher's exact test), Q value = 0.0098

Table S207.  Gene #74: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
19P LOSS MUTATED 23 16 24
19P LOSS WILD-TYPE 319 133 90

Figure S207.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'19p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00328 (Fisher's exact test), Q value = 0.043

Table S208.  Gene #74: '19p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
19P LOSS MUTATED 38 17
19P LOSS WILD-TYPE 410 69

Figure S208.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'19p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 3.85e-06 (Wilcoxon-test), Q value = 0.00081

Table S209.  Gene #74: '19p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
19P LOSS MUTATED 59 4.5 (5.9)
19P LOSS WILD-TYPE 514 2.0 (4.5)

Figure S209.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'19q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0319 (Fisher's exact test), Q value = 0.18

Table S210.  Gene #75: '19q loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
19Q LOSS MUTATED 7 0 2 12 1 2 4 1 5 8 7 5 1
19Q LOSS WILD-TYPE 97 1 34 159 9 1 22 20 74 46 54 22 1

Figure S210.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'19q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00163 (Fisher's exact test), Q value = 0.029

Table S211.  Gene #75: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
19Q LOSS MUTATED 24 10 21
19Q LOSS WILD-TYPE 318 139 93

Figure S211.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'19q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000625 (Wilcoxon-test), Q value = 0.015

Table S212.  Gene #75: '19q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
19Q LOSS MUTATED 51 4.5 (6.3)
19Q LOSS WILD-TYPE 522 2.0 (4.5)

Figure S212.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'21q loss' versus 'PRIMARY_SITE_OF_DISEASE'

P value = 0.00152 (Fisher's exact test), Q value = 0.028

Table S213.  Gene #78: '21q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

nPatients COLON RECTUM
ALL 442 162
21Q LOSS MUTATED 122 67
21Q LOSS WILD-TYPE 320 95

Figure S213.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #3: 'PRIMARY_SITE_OF_DISEASE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0116 (Fisher's exact test), Q value = 0.1

Table S214.  Gene #78: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
21Q LOSS MUTATED 92 51 47
21Q LOSS WILD-TYPE 250 98 67

Figure S214.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00026 (Fisher's exact test), Q value = 0.0098

Table S215.  Gene #78: '21q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
21Q LOSS MUTATED 114 8 62 3
21Q LOSS WILD-TYPE 267 52 84 10

Figure S215.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00396 (Wilcoxon-test), Q value = 0.05

Table S216.  Gene #78: '21q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
21Q LOSS MUTATED 182 3.3 (6.7)
21Q LOSS WILD-TYPE 391 1.7 (3.3)

Figure S216.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'22q loss' versus 'Time to Death'

P value = 0.0261 (logrank test), Q value = 0.17

Table S217.  Gene #79: '22q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 583 115 0.0 - 140.4 (19.1)
22Q LOSS MUTATED 187 43 0.2 - 140.4 (17.0)
22Q LOSS WILD-TYPE 396 72 0.0 - 139.2 (20.0)

Figure S217.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00745 (Fisher's exact test), Q value = 0.078

Table S218.  Gene #79: '22q loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 104 1 36 171 10 3 26 21 79 54 61 27 2
22Q LOSS MUTATED 24 0 9 46 1 1 9 11 29 22 30 11 0
22Q LOSS WILD-TYPE 80 1 27 125 9 2 17 10 50 32 31 16 2

Figure S218.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #4: 'NEOPLASM_DISEASESTAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.002

Table S219.  Gene #79: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
22Q LOSS MUTATED 85 67 46
22Q LOSS WILD-TYPE 257 82 68

Figure S219.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00359 (Fisher's exact test), Q value = 0.046

Table S220.  Gene #79: '22q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
22Q LOSS MUTATED 133 40
22Q LOSS WILD-TYPE 315 46

Figure S220.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0336 (Fisher's exact test), Q value = 0.19

Table S221.  Gene #79: '22q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
ALL 381 60 146 13
22Q LOSS MUTATED 132 10 51 4
22Q LOSS WILD-TYPE 249 50 95 9

Figure S221.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 8.96e-05 (Wilcoxon-test), Q value = 0.0045

Table S222.  Gene #79: '22q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
22Q LOSS MUTATED 187 2.9 (5.1)
22Q LOSS WILD-TYPE 386 1.9 (4.5)

Figure S222.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0287 (Fisher's exact test), Q value = 0.17

Table S223.  Gene #80: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 342 149 114
XP LOSS MUTATED 42 21 26
XP LOSS WILD-TYPE 300 128 88

Figure S223.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_N_STAGE'

'xp loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0487 (Fisher's exact test), Q value = 0.24

Table S224.  Gene #80: 'xp loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
XP LOSS MUTATED 61 19
XP LOSS WILD-TYPE 387 67

Figure S224.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

'xp loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0192 (Wilcoxon-test), Q value = 0.14

Table S225.  Gene #80: 'xp loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 573 2.2 (4.7)
XP LOSS MUTATED 85 3.2 (5.4)
XP LOSS WILD-TYPE 488 2.1 (4.6)

Figure S225.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'xq loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0134 (Fisher's exact test), Q value = 0.11

Table S226.  Gene #81: 'xq loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 448 86
XQ LOSS MUTATED 51 19
XQ LOSS WILD-TYPE 397 67

Figure S226.  Get High-res Image Gene #81: 'xq loss' versus Clinical Feature #7: 'PATHOLOGY_M_STAGE'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/15089878/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/COADREAD-TP/15076882/COADREAD-TP.merged_data.txt

  • Number of patients = 608

  • Number of significantly arm-level cnvs = 81

  • Number of selected clinical features = 13

  • Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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