Correlation between copy number variation genes (focal events) and selected clinical features
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 69 focal events and 12 clinical features across 443 patients, 269 significant findings detected with Q value < 0.25.

  • amp_2q33.1 cnv correlated to 'Time to Death',  'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_5p13.2 cnv correlated to 'PATHOLOGY_N_STAGE' and 'NUMBER_OF_LYMPH_NODES'.

  • amp_5q22.3 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • amp_6p21.1 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_7p21.2 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_8q12.1 cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • amp_8q24.21 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGY_M_STAGE'.

  • amp_11p15.5 cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_13q12.13 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'COMPLETENESS_OF_RESECTION', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_13q22.1 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'COMPLETENESS_OF_RESECTION', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_16p11.2 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_16q12.1 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_17q12 cnv correlated to 'PATHOLOGY_M_STAGE'.

  • amp_17q24.1 cnv correlated to 'Time to Death'.

  • amp_19p13.2 cnv correlated to 'PATHOLOGY_N_STAGE'.

  • amp_20p12.1 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'COMPLETENESS_OF_RESECTION'.

  • amp_20p11.21 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'COMPLETENESS_OF_RESECTION'.

  • amp_20q11.21 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_20q12 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • amp_20q13.12 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_1p36.11 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • del_1p33 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_1p13.1 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_1q43 cnv correlated to 'NEOPLASM_DISEASESTAGE'.

  • del_2q22.1 cnv correlated to 'NUMBER_OF_LYMPH_NODES' and 'RACE'.

  • del_3p26.2 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_3p14.2 cnv correlated to 'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_4p16.2 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION',  'COMPLETENESS_OF_RESECTION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_4q22.1 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_4q35.1 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_5q12.1 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_5q21.1 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_5q22.2 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_6p25.3 cnv correlated to 'YEARS_TO_BIRTH',  'GENDER', and 'RACE'.

  • del_6q26 cnv correlated to 'Time to Death',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'NUMBER_OF_LYMPH_NODES', and 'RACE'.

  • del_8p23.3 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_8p22 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE',  'COMPLETENESS_OF_RESECTION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_8q11.1 cnv correlated to 'RACE'.

  • del_9p21.3 cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • del_10p15.3 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_10q21.1 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'COMPLETENESS_OF_RESECTION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_10q23.31 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_10q25.2 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'COMPLETENESS_OF_RESECTION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_12p13.2 cnv correlated to 'Time to Death',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_13q14.13 cnv correlated to 'PATHOLOGY_N_STAGE' and 'RACE'.

  • del_14q31.1 cnv correlated to 'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_15q11.2 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_15q15.2 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_15q21.1 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_15q22.33 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'RADIATIONS_RADIATION_REGIMENINDICATION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_16p13.3 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_16q23.1 cnv correlated to 'Time to Death'.

  • del_17p12 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_17q24.3 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_18p11.31 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE',  'COMPLETENESS_OF_RESECTION', and 'NUMBER_OF_LYMPH_NODES'.

  • del_18q12.2 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_18q21.2 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'GENDER',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_19p13.3 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_20p12.1 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • del_21q11.2 cnv correlated to 'PATHOLOGY_N_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

  • del_22q13.32 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 69 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 269 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		RACE
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test
del 8p22 199 (45%) 244 0.162
(0.379) 		0.0318
(0.127) 		1e-05
(0.000517) 		0.053
(0.181) 		1e-05
(0.000517) 		2.17e-05
(0.000918) 		0.0558
(0.188) 		0.00758
(0.0468) 		0.59
(0.8) 		0.0403
(0.15) 		7.4e-07
(8.4e-05) 		0.383
(0.637)
del 1p36 11 164 (37%) 279 0.0457
(0.163) 		0.071
(0.227) 		0.00068
(0.00908) 		0.703
(0.857) 		0.00889
(0.0515) 		1.35e-05
(0.000659) 		0.14
(0.348) 		0.00138
(0.0147) 		1
(1.00) 		0.0907
(0.267) 		0.00256
(0.0241) 		0.0748
(0.235)
del 4p16 2 133 (30%) 310 0.0134
(0.0682) 		0.905
(0.983) 		0.00084
(0.0106) 		0.418
(0.668) 		0.00021
(0.00424) 		2.63e-05
(0.00104) 		0.535
(0.768) 		0.0346
(0.133) 		0.0266
(0.114) 		0.034
(0.133) 		8.63e-05
(0.00224) 		0.469
(0.71)
del 4q22 1 145 (33%) 298 0.028
(0.118) 		0.351
(0.614) 		0.00272
(0.0247) 		0.16
(0.377) 		0.00013
(0.00283) 		0.017
(0.0817) 		0.362
(0.624) 		0.0115
(0.0617) 		0.0346
(0.133) 		0.913
(0.99) 		7.86e-05
(0.00221) 		0.688
(0.855)
del 5q12 1 103 (23%) 340 0.113
(0.312) 		0.0667
(0.215) 		0.00792
(0.0479) 		0.839
(0.95) 		0.00926
(0.0523) 		0.0294
(0.122) 		0.311
(0.571) 		0.0498
(0.174) 		0.0123
(0.0648) 		0.73
(0.879) 		0.00339
(0.0281) 		0.417
(0.668)
del 10q21 1 94 (21%) 349 0.619
(0.817) 		0.0421
(0.153) 		0.00581
(0.0408) 		0.966
(1.00) 		0.00979
(0.054) 		0.00646
(0.042) 		1
(1.00) 		0.061
(0.2) 		0.115
(0.315) 		0.0661
(0.215) 		0.00401
(0.0316) 		0.646
(0.828)
del 18p11 31 241 (54%) 202 0.564
(0.784) 		0.0064
(0.042) 		0.00132
(0.0144) 		0.877
(0.969) 		0.0223
(0.102) 		2.22e-05
(0.000918) 		0.703
(0.857) 		1.74e-10
(1.44e-07) 		0.254
(0.52) 		0.026
(0.112) 		0.0255
(0.11) 		0.937
(1.00)
del 18q21 2 282 (64%) 161 0.736
(0.884) 		0.0349
(0.133) 		6e-05
(0.00184) 		0.803
(0.928) 		4e-05
(0.00138) 		3.53e-05
(0.00133) 		0.0606
(0.199) 		3.88e-09
(1.07e-06) 		0.557
(0.784) 		0.0851
(0.257) 		4.33e-05
(0.00138) 		0.813
(0.934)
amp 13q12 13 270 (61%) 173 0.876
(0.969) 		0.551
(0.784) 		9e-05
(0.00226) 		0.901
(0.982) 		0.00068
(0.00908) 		0.00058
(0.00815) 		0.77
(0.909) 		2.76e-07
(4.58e-05) 		0.284
(0.545) 		0.0222
(0.102) 		0.00251
(0.024) 		0.137
(0.345)
amp 13q22 1 274 (62%) 169 0.741
(0.888) 		0.608
(0.811) 		0.00011
(0.00268) 		0.895
(0.978) 		0.00039
(0.00687) 		0.00252
(0.024) 		0.281
(0.545) 		1.58e-06
(0.000131) 		0.291
(0.549) 		0.046
(0.163) 		0.00299
(0.0263) 		0.117
(0.317)
del 1p33 120 (27%) 323 0.00278
(0.0251) 		0.911
(0.988) 		0.0155
(0.0761) 		0.304
(0.565) 		0.0155
(0.0761) 		0.00473
(0.0356) 		0.454
(0.697) 		0.0602
(0.199) 		0.566
(0.784) 		0.246
(0.51) 		0.005
(0.0363) 		0.372
(0.628)
del 8p23 3 185 (42%) 258 0.626
(0.82) 		0.135
(0.343) 		0.00112
(0.0125) 		0.141
(0.349) 		8e-05
(0.00221) 		0.000438
(0.00712) 		0.0159
(0.0772) 		0.0246
(0.108) 		0.574
(0.789) 		0.0892
(0.265) 		4.19e-05
(0.00138) 		0.366
(0.624)
del 10q25 2 106 (24%) 337 0.104
(0.291) 		0.0663
(0.215) 		0.0295
(0.122) 		0.38
(0.635) 		0.00774
(0.0475) 		0.00986
(0.0541) 		1
(1.00) 		0.103
(0.29) 		0.144
(0.352) 		0.0751
(0.235) 		0.00383
(0.0305) 		1
(1.00)
del 15q11 2 173 (39%) 270 0.65
(0.832) 		0.484
(0.724) 		0.01
(0.0541) 		0.961
(1.00) 		0.00873
(0.0509) 		0.00422
(0.0324) 		0.698
(0.855) 		0.0456
(0.163) 		0.0589
(0.196) 		0.438
(0.686) 		0.00493
(0.0361) 		0.306
(0.565)
del 15q15 2 168 (38%) 275 0.481
(0.72) 		0.159
(0.375) 		0.0138
(0.0699) 		0.954
(1.00) 		0.00649
(0.042) 		0.000501
(0.0076) 		0.769
(0.909) 		0.0317
(0.127) 		0.0539
(0.183) 		0.284
(0.545) 		0.00929
(0.0523) 		0.254
(0.52)
del 15q21 1 165 (37%) 278 0.32
(0.578) 		0.458
(0.7) 		0.0692
(0.222) 		0.971
(1.00) 		0.0336
(0.133) 		0.000847
(0.0106) 		0.556
(0.784) 		0.0437
(0.158) 		0.0511
(0.175) 		0.176
(0.408) 		0.0349
(0.133) 		0.139
(0.347)
del 15q22 33 157 (35%) 286 0.695
(0.855) 		0.305
(0.565) 		0.00679
(0.0432) 		0.585
(0.795) 		0.00725
(0.0451) 		0.000456
(0.00727) 		0.691
(0.855) 		0.0421
(0.153) 		0.044
(0.158) 		0.417
(0.668) 		0.00617
(0.0415) 		0.183
(0.419)
del 17p12 248 (56%) 195 0.506
(0.744) 		0.0174
(0.0832) 		2e-05
(0.000918) 		0.88
(0.972) 		1e-05
(0.000517) 		0.00025
(0.00482) 		0.214
(0.472) 		5.14e-06
(0.000327) 		0.259
(0.524) 		0.132
(0.336) 		8.59e-07
(8.4e-05) 		0.806
(0.929)
del 18q12 2 268 (60%) 175 0.682
(0.853) 		0.0177
(0.0844) 		0.00056
(0.00799) 		0.802
(0.928) 		0.00087
(0.0108) 		0.000911
(0.0111) 		0.175
(0.406) 		3.04e-09
(1.07e-06) 		0.281
(0.545) 		0.102
(0.289) 		0.00158
(0.0162) 		0.883
(0.972)
amp 7p21 2 251 (57%) 192 0.788
(0.917) 		0.0912
(0.267) 		0.00012
(0.00269) 		0.393
(0.648) 		7e-05
(0.00207) 		0.0116
(0.0618) 		0.924
(0.997) 		0.0348
(0.133) 		0.262
(0.527) 		0.261
(0.527) 		0.000235
(0.00464) 		0.533
(0.768)
amp 20p12 1 206 (47%) 237 0.0723
(0.23) 		0.895
(0.978) 		0.00113
(0.0125) 		0.734
(0.882) 		0.303
(0.565) 		0.000752
(0.00988) 		0.216
(0.472) 		0.0364
(0.137) 		0.0998
(0.287) 		0.0249
(0.109) 		0.268
(0.533) 		0.401
(0.654)
amp 20q11 21 317 (72%) 126 0.984
(1.00) 		0.429
(0.679) 		0.0025
(0.024) 		0.289
(0.549) 		0.00623
(0.0416) 		0.00316
(0.0267) 		0.292
(0.551) 		9.13e-07
(8.4e-05) 		0.561
(0.784) 		0.089
(0.265) 		0.0127
(0.0664) 		0.783
(0.914)
amp 20q12 318 (72%) 125 0.854
(0.96) 		0.431
(0.68) 		0.00099
(0.0119) 		0.394
(0.648) 		0.00846
(0.05) 		0.00105
(0.0122) 		0.245
(0.51) 		1.52e-07
(3.14e-05) 		0.562
(0.784) 		0.0901
(0.266) 		0.0133
(0.0682) 		0.686
(0.855)
amp 20q13 12 320 (72%) 123 0.875
(0.969) 		0.528
(0.764) 		0.00041
(0.00693) 		0.564
(0.784) 		0.00414
(0.032) 		0.000505
(0.0076) 		0.243
(0.51) 		6.1e-07
(8.4e-05) 		0.564
(0.784) 		0.0914
(0.267) 		0.00405
(0.0316) 		0.604
(0.81)
del 3p26 2 69 (16%) 374 0.137
(0.345) 		0.449
(0.694) 		0.0568
(0.19) 		0.141
(0.349) 		0.00952
(0.0529) 		0.00347
(0.0285) 		0.896
(0.978) 		0.0367
(0.137) 		1
(1.00) 		0.34
(0.6) 		0.00616
(0.0415) 		0.825
(0.944)
del 4q35 1 153 (35%) 290 0.545
(0.779) 		0.0819
(0.251) 		0.0499
(0.174) 		0.317
(0.575) 		0.00111
(0.0125) 		0.00857
(0.0503) 		0.317
(0.575) 		0.109
(0.303) 		0.0407
(0.15) 		0.381
(0.635) 		0.000314
(0.00577) 		0.241
(0.507)
del 5q21 1 124 (28%) 319 0.181
(0.417) 		0.115
(0.315) 		0.0004
(0.0069) 		0.996
(1.00) 		0.00109
(0.0125) 		0.00812
(0.0486) 		0.341
(0.6) 		0.442
(0.689) 		0.0215
(0.0997) 		0.458
(0.7) 		0.000264
(0.00496) 		0.44
(0.687)
del 5q22 2 127 (29%) 316 0.152
(0.365) 		0.188
(0.427) 		0.024
(0.107) 		1
(1.00) 		0.0285
(0.119) 		0.00312
(0.0267) 		0.141
(0.349) 		0.125
(0.33) 		0.0232
(0.105) 		0.126
(0.33) 		0.0117
(0.0619) 		0.362
(0.624)
del 6q26 61 (14%) 382 0.0185
(0.0876) 		0.896
(0.978) 		0.116
(0.315) 		0.429
(0.679) 		0.00285
(0.0254) 		0.0245
(0.108) 		0.679
(0.851) 		1
(1.00) 		1
(1.00) 		0.15
(0.362) 		0.00105
(0.0122) 		0.053
(0.181)
del 10p15 3 77 (17%) 366 0.771
(0.909) 		0.438
(0.686) 		0.0014
(0.0147) 		0.93
(1.00) 		0.00927
(0.0523) 		0.000814
(0.0105) 		0.802
(0.928) 		0.465
(0.706) 		0.0795
(0.246) 		0.656
(0.834) 		0.0026
(0.0242) 		0.509
(0.744)
del 10q23 31 106 (24%) 337 0.875
(0.969) 		0.00371
(0.0299) 		0.00316
(0.0267) 		0.887
(0.976) 		0.0263
(0.113) 		0.00944
(0.0528) 		0.578
(0.789) 		0.103
(0.29) 		0.144
(0.352) 		0.19
(0.43) 		0.00526
(0.0379) 		0.788
(0.917)
del 12p13 2 59 (13%) 384 0.0231
(0.105) 		0.224
(0.485) 		0.132
(0.336) 		0.883
(0.972) 		0.0583
(0.195) 		0.0357
(0.136) 		0.781
(0.914) 		0.0128
(0.0664) 		1
(1.00) 		0.473
(0.714) 		0.0668
(0.215) 		0.728
(0.877)
del 17q24 3 69 (16%) 374 0.0809
(0.249) 		0.305
(0.565) 		0.00642
(0.042) 		0.257
(0.523) 		0.00182
(0.0182) 		0.00146
(0.0151) 		0.36
(0.624) 		0.848
(0.957) 		1
(1.00) 		0.39
(0.645) 		8.66e-05
(0.00224) 		0.289
(0.549)
del 22q13 32 156 (35%) 287 0.152
(0.365) 		0.321
(0.578) 		0.00562
(0.0398) 		0.563
(0.784) 		0.00018
(0.00382) 		0.00372
(0.0299) 		0.765
(0.909) 		0.00337
(0.0281) 		1
(1.00) 		0.577
(0.789) 		0.000117
(0.00269) 		0.353
(0.615)
amp 6p21 1 96 (22%) 347 0.99
(1.00) 		0.698
(0.855) 		0.0328
(0.131) 		0.622
(0.818) 		0.00816
(0.0486) 		0.24
(0.506) 		0.356
(0.617) 		0.237
(0.503) 		0.00993
(0.0541) 		0.637
(0.825) 		0.00716
(0.0451) 		0.216
(0.472)
amp 11p15 5 91 (21%) 352 0.779
(0.914) 		0.0156
(0.0761) 		0.349
(0.612) 		0.156
(0.372) 		0.0419
(0.153) 		0.125
(0.33) 		0.724
(0.874) 		0.00315
(0.0267) 		0.109
(0.303) 		0.452
(0.695) 		0.0279
(0.118) 		0.265
(0.53)
amp 16p11 2 123 (28%) 320 0.693
(0.855) 		0.222
(0.482) 		0.00056
(0.00799) 		0.583
(0.794) 		0.00021
(0.00424) 		0.212
(0.47) 		0.596
(0.807) 		0.0078
(0.0475) 		1
(1.00) 		0.665
(0.84) 		0.000116
(0.00269) 		0.443
(0.69)
amp 16q12 1 109 (25%) 334 0.159
(0.375) 		0.0852
(0.257) 		0.00048
(0.0075) 		0.942
(1.00) 		0.00063
(0.00869) 		0.626
(0.82) 		0.508
(0.744) 		0.0146
(0.0736) 		0.572
(0.789) 		0.636
(0.825) 		0.000328
(0.0059) 		0.212
(0.47)
amp 20p11 21 248 (56%) 195 0.355
(0.617) 		0.531
(0.765) 		0.00179
(0.0181) 		0.751
(0.897) 		0.192
(0.432) 		0.000435
(0.00712) 		0.293
(0.552) 		0.00191
(0.0189) 		0.259
(0.524) 		0.0193
(0.0904) 		0.315
(0.575) 		0.768
(0.909)
del 1p13 1 115 (26%) 328 0.102
(0.289) 		0.465
(0.706) 		0.00594
(0.0413) 		0.488
(0.727) 		0.0043
(0.0327) 		0.00267
(0.0245) 		0.235
(0.502) 		0.0825
(0.251) 		1
(1.00) 		0.131
(0.336) 		0.000557
(0.00799) 		0.304
(0.565)
del 14q31 1 145 (33%) 298 0.675
(0.848) 		0.201
(0.451) 		0.217
(0.472) 		0.31
(0.57) 		0.0233
(0.105) 		0.00491
(0.0361) 		0.479
(0.719) 		5.09e-06
(0.000327) 		0.554
(0.784) 		0.316
(0.575) 		0.0128
(0.0664) 		0.956
(1.00)
del 16p13 3 54 (12%) 389 0.00603
(0.0413) 		0.518
(0.754) 		0.0305
(0.126) 		0.0315
(0.127) 		0.127
(0.33) 		0.129
(0.336) 		0.665
(0.84) 		1
(1.00) 		1
(1.00) 		0.333
(0.594) 		0.0736
(0.233) 		0.338
(0.599)
del 19p13 3 62 (14%) 381 0.369
(0.625) 		0.118
(0.318) 		0.00723
(0.0451) 		0.807
(0.929) 		4e-05
(0.00138) 		0.0149
(0.0748) 		0.273
(0.538) 		0.229
(0.492) 		0.365
(0.624) 		0.0853
(0.257) 		2.68e-06
(0.000202) 		0.94
(1.00)
amp 2q33 1 89 (20%) 354 0.0318
(0.127) 		0.555
(0.784) 		0.25
(0.513) 		0.787
(0.917) 		0.00598
(0.0413) 		0.374
(0.629) 		0.478
(0.719) 		0.604
(0.81) 		0.491
(0.728) 		0.119
(0.32) 		0.00482
(0.0359) 		0.364
(0.624)
del 3p14 2 85 (19%) 358 0.665
(0.84) 		0.308
(0.569) 		0.229
(0.492) 		0.111
(0.307) 		0.0472
(0.166) 		0.0741
(0.234) 		0.547
(0.781) 		0.481
(0.72) 		1
(1.00) 		0.635
(0.825) 		0.0197
(0.0918) 		0.832
(0.946)
del 6p25 3 54 (12%) 389 0.149
(0.361) 		0.0759
(0.236) 		0.667
(0.84) 		0.408
(0.661) 		0.829
(0.945) 		0.522
(0.758) 		0.0596
(0.197) 		0.4
(0.654) 		1
(1.00) 		0.394
(0.648) 		0.857
(0.962) 		0.0154
(0.0761)
del 21q11 2 137 (31%) 306 0.336
(0.596) 		0.851
(0.958) 		0.284
(0.545) 		0.381
(0.635) 		0.0272
(0.116) 		0.131
(0.336) 		0.918
(0.994) 		0.00141
(0.0147) 		0.227
(0.49) 		0.627
(0.82) 		0.0309
(0.126) 		0.498
(0.737)
amp 5p13 2 86 (19%) 357 0.922
(0.997) 		0.0966
(0.282) 		0.246
(0.51) 		0.534
(0.768) 		0.0338
(0.133) 		0.154
(0.368) 		0.471
(0.712) 		0.863
(0.965) 		1
(1.00) 		0.149
(0.362) 		0.0186
(0.0876) 		0.3
(0.562)
amp 8q12 1 231 (52%) 212 0.77
(0.909) 		0.0503
(0.175) 		0.643
(0.827) 		0.655
(0.834) 		0.508
(0.744) 		0.127
(0.33) 		0.507
(0.744) 		0.0509
(0.175) 		0.25
(0.513) 		0.446
(0.692) 		0.317
(0.575) 		0.622
(0.818)
amp 8q24 21 255 (58%) 188 0.704
(0.857) 		0.0554
(0.187) 		0.0982
(0.285) 		0.379
(0.634) 		0.279
(0.544) 		0.0246
(0.108) 		0.29
(0.549) 		0.124
(0.33) 		0.265
(0.53) 		0.365
(0.624) 		0.214
(0.472) 		0.536
(0.768)
del 2q22 1 24 (5%) 419 0.698
(0.855) 		0.744
(0.891) 		0.236
(0.503) 		0.238
(0.503) 		0.0822
(0.251) 		1
(1.00) 		0.676
(0.848) 		1
(1.00) 		1
(1.00) 		0.643
(0.827) 		0.00925
(0.0523) 		0.00659
(0.0423)
del 9p21 3 59 (13%) 384 0.873
(0.969) 		0.0359
(0.136) 		0.841
(0.951) 		0.365
(0.624) 		0.33
(0.591) 		0.549
(0.783) 		0.207
(0.464) 		0.041
(0.151) 		1
(1.00) 		0.643
(0.827) 		0.1
(0.287) 		0.377
(0.634)
del 13q14 13 19 (4%) 424 0.996
(1.00) 		0.189
(0.43) 		0.276
(0.541) 		0.71
(0.86) 		0.0344
(0.133) 		1
(1.00) 		0.815
(0.936) 		1
(1.00) 		1
(1.00) 		0.872
(0.969) 		0.138
(0.346) 		0.0366
(0.137)
amp 5q22 3 44 (10%) 399 0.426
(0.677) 		0.893
(0.978) 		0.599
(0.807) 		0.943
(1.00) 		0.372
(0.628) 		0.0311
(0.127) 		0.527
(0.764) 		0.244
(0.51) 		0.27
(0.535) 		0.0872
(0.261) 		0.234
(0.5) 		0.503
(0.742)
amp 17q12 112 (25%) 331 0.118
(0.318) 		0.273
(0.538) 		0.179
(0.414) 		0.123
(0.327) 		0.132
(0.336) 		0.0056
(0.0398) 		0.276
(0.541) 		0.423
(0.675) 		1
(1.00) 		0.145
(0.355) 		0.112
(0.309) 		0.368
(0.625)
amp 17q24 1 104 (23%) 339 0.0153
(0.0761) 		0.448
(0.693) 		0.609
(0.811) 		0.332
(0.593) 		0.438
(0.686) 		0.184
(0.421) 		0.576
(0.789) 		0.138
(0.346) 		0.553
(0.784) 		0.265
(0.53) 		0.826
(0.944) 		0.84
(0.951)
amp 19p13 2 75 (17%) 368 0.929
(1.00) 		0.943
(1.00) 		0.833
(0.946) 		0.713
(0.862) 		0.0505
(0.175) 		0.328
(0.589) 		0.101
(0.288) 		0.466
(0.707) 		0.428
(0.678) 		0.116
(0.315) 		0.643
(0.827) 		0.872
(0.969)
del 1q43 52 (12%) 391 0.464
(0.706) 		0.264
(0.53) 		0.0761
(0.236) 		0.122
(0.326) 		0.509
(0.744) 		0.372
(0.628) 		0.66
(0.837) 		0.83
(0.945) 		0.313
(0.573) 		0.435
(0.684) 		0.286
(0.548) 		0.157
(0.374)
del 8q11 1 30 (7%) 413 0.933
(1.00) 		0.41
(0.661) 		0.127
(0.33) 		0.597
(0.807) 		0.132
(0.336) 		0.404
(0.657) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.446
(0.692) 		0.0999
(0.287) 		0.0467
(0.165)
del 16q23 1 58 (13%) 385 0.0248
(0.109) 		0.849
(0.957) 		0.837
(0.95) 		0.557
(0.784) 		0.651
(0.832) 		0.414
(0.665) 		0.328
(0.589) 		0.411
(0.661) 		1
(1.00) 		0.791
(0.919) 		0.49
(0.728) 		0.184
(0.42)
del 20p12 1 83 (19%) 360 0.216
(0.472) 		0.66
(0.837) 		0.501
(0.74) 		0.559
(0.784) 		0.295
(0.554) 		1
(1.00) 		0.903
(0.983) 		0.0744
(0.234) 		1
(1.00) 		0.642
(0.827) 		0.182
(0.419) 		0.346
(0.608)
amp 8p11 23 156 (35%) 287 0.711
(0.86) 		0.33
(0.591) 		0.491
(0.728) 		0.782
(0.914) 		0.699
(0.855) 		0.772
(0.909) 		0.692
(0.855) 		0.247
(0.512) 		0.284
(0.545) 		0.667
(0.84) 		0.687
(0.855) 		0.696
(0.855)
amp 8p11 21 185 (42%) 258 0.888
(0.976) 		0.266
(0.53) 		0.53
(0.765) 		0.612
(0.811) 		0.576
(0.789) 		0.4
(0.654) 		0.211
(0.47) 		0.401
(0.654) 		0.574
(0.789) 		0.257
(0.523) 		0.612
(0.811) 		0.352
(0.615)
amp 12p13 33 111 (25%) 332 0.0997
(0.287) 		0.282
(0.545) 		0.109
(0.303) 		0.148
(0.359) 		0.281
(0.545) 		0.63
(0.822) 		0.826
(0.944) 		0.873
(0.969) 		0.576
(0.789) 		0.451
(0.695) 		0.41
(0.661) 		0.59
(0.8)
amp 17p11 2 44 (10%) 399 0.454
(0.697) 		0.61
(0.811) 		0.621
(0.818) 		0.566
(0.784) 		0.757
(0.901) 		0.646
(0.828) 		0.634
(0.825) 		1
(1.00) 		1
(1.00) 		0.804
(0.928) 		0.693
(0.855) 		0.168
(0.391)
amp 19q13 11 94 (21%) 349 0.408
(0.661) 		0.968
(1.00) 		0.82
(0.94) 		0.653
(0.833) 		0.158
(0.374) 		0.223
(0.482) 		0.132
(0.336) 		0.614
(0.812) 		0.512
(0.746) 		0.782
(0.914) 		0.684
(0.854) 		0.945
(1.00)
del 2p21 16 (4%) 427 0.605
(0.81) 		0.361
(0.624) 		0.163
(0.381) 		0.581
(0.793) 		0.288
(0.549) 		0.0859
(0.258) 		0.612
(0.811) 		0.708
(0.86) 		1
(1.00) 		0.63
(0.822) 		0.341
(0.6) 		0.767
(0.909)
del 3q26 31 44 (10%) 399 0.6
(0.807) 		0.39
(0.645) 		0.211
(0.47) 		0.193
(0.433) 		0.275
(0.54) 		0.249
(0.513) 		0.752
(0.897) 		0.244
(0.51) 		1
(1.00) 		0.774
(0.91) 		0.424
(0.676) 		0.873
(0.969)
del 7q31 1 12 (3%) 431 0.978
(1.00) 		0.973
(1.00) 		0.707
(0.859) 		0.606
(0.81) 		1
(1.00) 		0.699
(0.855) 		0.562
(0.784) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.859
(0.962) 		0.387
(0.643)
'amp_2q33.1' versus 'Time to Death'

P value = 0.0318 (logrank test), Q value = 0.13

Table S1.  Gene #1: 'amp_2q33.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
AMP PEAK 1(2Q33.1) MUTATED 84 22 0.0 - 74.6 (20.7)
AMP PEAK 1(2Q33.1) WILD-TYPE 346 71 0.0 - 140.4 (20.4)

Figure S1.  Get High-res Image Gene #1: 'amp_2q33.1' versus Clinical Feature #1: 'Time to Death'

'amp_2q33.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00598 (Fisher's exact test), Q value = 0.041

Table S2.  Gene #1: 'amp_2q33.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 1(2Q33.1) MUTATED 40 22 26
AMP PEAK 1(2Q33.1) WILD-TYPE 217 82 55

Figure S2.  Get High-res Image Gene #1: 'amp_2q33.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_2q33.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00482 (Wilcoxon-test), Q value = 0.036

Table S3.  Gene #1: 'amp_2q33.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 1(2Q33.1) MUTATED 85 2.9 (4.5)
AMP PEAK 1(2Q33.1) WILD-TYPE 333 1.9 (4.4)

Figure S3.  Get High-res Image Gene #1: 'amp_2q33.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'amp_5p13.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0338 (Fisher's exact test), Q value = 0.13

Table S4.  Gene #2: 'amp_5p13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 2(5P13.2) MUTATED 42 20 24
AMP PEAK 2(5P13.2) WILD-TYPE 215 84 57

Figure S4.  Get High-res Image Gene #2: 'amp_5p13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_5p13.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0186 (Wilcoxon-test), Q value = 0.088

Table S5.  Gene #2: 'amp_5p13.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 2(5P13.2) MUTATED 83 3.0 (4.6)
AMP PEAK 2(5P13.2) WILD-TYPE 335 1.9 (4.4)

Figure S5.  Get High-res Image Gene #2: 'amp_5p13.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'amp_5q22.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0311 (Fisher's exact test), Q value = 0.13

Table S6.  Gene #3: 'amp_5q22.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
AMP PEAK 3(5Q22.3) MUTATED 26 11
AMP PEAK 3(5Q22.3) WILD-TYPE 296 51

Figure S6.  Get High-res Image Gene #3: 'amp_5q22.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_6p21.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0328 (Fisher's exact test), Q value = 0.13

Table S7.  Gene #4: 'amp_6p21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
AMP PEAK 4(6P21.1) MUTATED 13 0 1 24 1 0 4 6 15 13 10 6 1
AMP PEAK 4(6P21.1) WILD-TYPE 61 1 27 107 7 1 17 6 41 26 33 12 1

Figure S7.  Get High-res Image Gene #4: 'amp_6p21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_6p21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00816 (Fisher's exact test), Q value = 0.049

Table S8.  Gene #4: 'amp_6p21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 4(6P21.1) MUTATED 46 22 28
AMP PEAK 4(6P21.1) WILD-TYPE 211 82 53

Figure S8.  Get High-res Image Gene #4: 'amp_6p21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_6p21.1' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00993 (Fisher's exact test), Q value = 0.054

Table S9.  Gene #4: 'amp_6p21.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
AMP PEAK 4(6P21.1) MUTATED 3 93
AMP PEAK 4(6P21.1) WILD-TYPE 0 347

Figure S9.  Get High-res Image Gene #4: 'amp_6p21.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'amp_6p21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00716 (Wilcoxon-test), Q value = 0.045

Table S10.  Gene #4: 'amp_6p21.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 4(6P21.1) MUTATED 93 3.3 (5.6)
AMP PEAK 4(6P21.1) WILD-TYPE 325 1.7 (4.0)

Figure S10.  Get High-res Image Gene #4: 'amp_6p21.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'amp_7p21.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0027

Table S11.  Gene #5: 'amp_7p21.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
AMP PEAK 5(7P21.2) MUTATED 40 1 15 54 2 0 13 11 38 26 30 14 1
AMP PEAK 5(7P21.2) WILD-TYPE 34 0 13 77 6 1 8 1 18 13 13 4 1

Figure S11.  Get High-res Image Gene #5: 'amp_7p21.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_7p21.2' versus 'PATHOLOGY_N_STAGE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0021

Table S12.  Gene #5: 'amp_7p21.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 5(7P21.2) MUTATED 123 71 56
AMP PEAK 5(7P21.2) WILD-TYPE 134 33 25

Figure S12.  Get High-res Image Gene #5: 'amp_7p21.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_7p21.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0116 (Fisher's exact test), Q value = 0.062

Table S13.  Gene #5: 'amp_7p21.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
AMP PEAK 5(7P21.2) MUTATED 171 44
AMP PEAK 5(7P21.2) WILD-TYPE 151 18

Figure S13.  Get High-res Image Gene #5: 'amp_7p21.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_7p21.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0348 (Fisher's exact test), Q value = 0.13

Table S14.  Gene #5: 'amp_7p21.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 5(7P21.2) MUTATED 224 26
AMP PEAK 5(7P21.2) WILD-TYPE 157 34

Figure S14.  Get High-res Image Gene #5: 'amp_7p21.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_7p21.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000235 (Wilcoxon-test), Q value = 0.0046

Table S15.  Gene #5: 'amp_7p21.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 5(7P21.2) MUTATED 242 2.5 (4.8)
AMP PEAK 5(7P21.2) WILD-TYPE 176 1.6 (3.9)

Figure S15.  Get High-res Image Gene #5: 'amp_7p21.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'amp_8q12.1' versus 'YEARS_TO_BIRTH'

P value = 0.0503 (Wilcoxon-test), Q value = 0.17

Table S16.  Gene #8: 'amp_8q12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
AMP PEAK 8(8Q12.1) MUTATED 230 66.0 (12.5)
AMP PEAK 8(8Q12.1) WILD-TYPE 211 68.0 (13.5)

Figure S16.  Get High-res Image Gene #8: 'amp_8q12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q12.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0509 (Fisher's exact test), Q value = 0.18

Table S17.  Gene #8: 'amp_8q12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 8(8Q12.1) MUTATED 207 24
AMP PEAK 8(8Q12.1) WILD-TYPE 174 36

Figure S17.  Get High-res Image Gene #8: 'amp_8q12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_8q24.21' versus 'YEARS_TO_BIRTH'

P value = 0.0554 (Wilcoxon-test), Q value = 0.19

Table S18.  Gene #9: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
AMP PEAK 9(8Q24.21) MUTATED 254 66.0 (12.8)
AMP PEAK 9(8Q24.21) WILD-TYPE 187 68.2 (13.2)

Figure S18.  Get High-res Image Gene #9: 'amp_8q24.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.21' versus 'PATHOLOGY_M_STAGE'

P value = 0.0246 (Fisher's exact test), Q value = 0.11

Table S19.  Gene #9: 'amp_8q24.21' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
AMP PEAK 9(8Q24.21) MUTATED 178 44
AMP PEAK 9(8Q24.21) WILD-TYPE 144 18

Figure S19.  Get High-res Image Gene #9: 'amp_8q24.21' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.0156 (Wilcoxon-test), Q value = 0.076

Table S20.  Gene #10: 'amp_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
AMP PEAK 10(11P15.5) MUTATED 91 64.1 (12.6)
AMP PEAK 10(11P15.5) WILD-TYPE 350 67.7 (13.0)

Figure S20.  Get High-res Image Gene #10: 'amp_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_11p15.5' versus 'PATHOLOGY_N_STAGE'

P value = 0.0419 (Fisher's exact test), Q value = 0.15

Table S21.  Gene #10: 'amp_11p15.5' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 10(11P15.5) MUTATED 42 26 22
AMP PEAK 10(11P15.5) WILD-TYPE 215 78 59

Figure S21.  Get High-res Image Gene #10: 'amp_11p15.5' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_11p15.5' versus 'HISTOLOGICAL_TYPE'

P value = 0.00315 (Fisher's exact test), Q value = 0.027

Table S22.  Gene #10: 'amp_11p15.5' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 10(11P15.5) MUTATED 85 4
AMP PEAK 10(11P15.5) WILD-TYPE 296 56

Figure S22.  Get High-res Image Gene #10: 'amp_11p15.5' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_11p15.5' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0279 (Wilcoxon-test), Q value = 0.12

Table S23.  Gene #10: 'amp_11p15.5' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 10(11P15.5) MUTATED 85 2.8 (6.2)
AMP PEAK 10(11P15.5) WILD-TYPE 333 1.9 (3.9)

Figure S23.  Get High-res Image Gene #10: 'amp_11p15.5' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'amp_13q12.13' versus 'NEOPLASM_DISEASESTAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0023

Table S24.  Gene #12: 'amp_13q12.13' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
AMP PEAK 12(13Q12.13) MUTATED 43 0 14 68 2 1 11 11 39 25 36 15 0
AMP PEAK 12(13Q12.13) WILD-TYPE 31 1 14 63 6 0 10 1 17 14 7 3 2

Figure S24.  Get High-res Image Gene #12: 'amp_13q12.13' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_13q12.13' versus 'PATHOLOGY_N_STAGE'

P value = 0.00068 (Fisher's exact test), Q value = 0.0091

Table S25.  Gene #12: 'amp_13q12.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 12(13Q12.13) MUTATED 138 76 56
AMP PEAK 12(13Q12.13) WILD-TYPE 119 28 25

Figure S25.  Get High-res Image Gene #12: 'amp_13q12.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_13q12.13' versus 'PATHOLOGY_M_STAGE'

P value = 0.00058 (Fisher's exact test), Q value = 0.0081

Table S26.  Gene #12: 'amp_13q12.13' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
AMP PEAK 12(13Q12.13) MUTATED 186 50
AMP PEAK 12(13Q12.13) WILD-TYPE 136 12

Figure S26.  Get High-res Image Gene #12: 'amp_13q12.13' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_13q12.13' versus 'HISTOLOGICAL_TYPE'

P value = 2.76e-07 (Fisher's exact test), Q value = 4.6e-05

Table S27.  Gene #12: 'amp_13q12.13' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 12(13Q12.13) MUTATED 251 18
AMP PEAK 12(13Q12.13) WILD-TYPE 130 42

Figure S27.  Get High-res Image Gene #12: 'amp_13q12.13' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_13q12.13' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0222 (Fisher's exact test), Q value = 0.1

Table S28.  Gene #12: 'amp_13q12.13' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
AMP PEAK 12(13Q12.13) MUTATED 191 1 19 10
AMP PEAK 12(13Q12.13) WILD-TYPE 125 2 5 15

Figure S28.  Get High-res Image Gene #12: 'amp_13q12.13' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'amp_13q12.13' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00251 (Wilcoxon-test), Q value = 0.024

Table S29.  Gene #12: 'amp_13q12.13' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 12(13Q12.13) MUTATED 260 2.4 (4.8)
AMP PEAK 12(13Q12.13) WILD-TYPE 158 1.5 (3.7)

Figure S29.  Get High-res Image Gene #12: 'amp_13q12.13' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'amp_13q22.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0027

Table S30.  Gene #13: 'amp_13q22.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
AMP PEAK 13(13Q22.1) MUTATED 45 0 15 66 2 1 12 11 39 27 35 15 0
AMP PEAK 13(13Q22.1) WILD-TYPE 29 1 13 65 6 0 9 1 17 12 8 3 2

Figure S30.  Get High-res Image Gene #13: 'amp_13q22.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_13q22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00039 (Fisher's exact test), Q value = 0.0069

Table S31.  Gene #13: 'amp_13q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 13(13Q22.1) MUTATED 139 77 57
AMP PEAK 13(13Q22.1) WILD-TYPE 118 27 24

Figure S31.  Get High-res Image Gene #13: 'amp_13q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_13q22.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.00252 (Fisher's exact test), Q value = 0.024

Table S32.  Gene #13: 'amp_13q22.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
AMP PEAK 13(13Q22.1) MUTATED 188 49
AMP PEAK 13(13Q22.1) WILD-TYPE 134 13

Figure S32.  Get High-res Image Gene #13: 'amp_13q22.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_13q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.00013

Table S33.  Gene #13: 'amp_13q22.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 13(13Q22.1) MUTATED 253 20
AMP PEAK 13(13Q22.1) WILD-TYPE 128 40

Figure S33.  Get High-res Image Gene #13: 'amp_13q22.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_13q22.1' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.046 (Fisher's exact test), Q value = 0.16

Table S34.  Gene #13: 'amp_13q22.1' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
AMP PEAK 13(13Q22.1) MUTATED 193 1 18 10
AMP PEAK 13(13Q22.1) WILD-TYPE 123 2 6 15

Figure S34.  Get High-res Image Gene #13: 'amp_13q22.1' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'amp_13q22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00299 (Wilcoxon-test), Q value = 0.026

Table S35.  Gene #13: 'amp_13q22.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 13(13Q22.1) MUTATED 265 2.4 (4.8)
AMP PEAK 13(13Q22.1) WILD-TYPE 153 1.6 (3.7)

Figure S35.  Get High-res Image Gene #13: 'amp_13q22.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'amp_16p11.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00056 (Fisher's exact test), Q value = 0.008

Table S36.  Gene #14: 'amp_16p11.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
AMP PEAK 14(16P11.2) MUTATED 14 1 3 29 1 0 5 9 20 16 15 5 1
AMP PEAK 14(16P11.2) WILD-TYPE 60 0 25 102 7 1 16 3 36 23 28 13 1

Figure S36.  Get High-res Image Gene #14: 'amp_16p11.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_16p11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0042

Table S37.  Gene #14: 'amp_16p11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 14(16P11.2) MUTATED 53 37 33
AMP PEAK 14(16P11.2) WILD-TYPE 204 67 48

Figure S37.  Get High-res Image Gene #14: 'amp_16p11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_16p11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0078 (Fisher's exact test), Q value = 0.047

Table S38.  Gene #14: 'amp_16p11.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 14(16P11.2) MUTATED 114 8
AMP PEAK 14(16P11.2) WILD-TYPE 267 52

Figure S38.  Get High-res Image Gene #14: 'amp_16p11.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_16p11.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000116 (Wilcoxon-test), Q value = 0.0027

Table S39.  Gene #14: 'amp_16p11.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 14(16P11.2) MUTATED 118 3.3 (6.2)
AMP PEAK 14(16P11.2) WILD-TYPE 300 1.6 (3.4)

Figure S39.  Get High-res Image Gene #14: 'amp_16p11.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'amp_16q12.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00048 (Fisher's exact test), Q value = 0.0075

Table S40.  Gene #15: 'amp_16q12.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
AMP PEAK 15(16Q12.1) MUTATED 14 1 3 22 1 0 5 9 20 14 11 4 1
AMP PEAK 15(16Q12.1) WILD-TYPE 60 0 25 109 7 1 16 3 36 25 32 14 1

Figure S40.  Get High-res Image Gene #15: 'amp_16q12.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_16q12.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00063 (Fisher's exact test), Q value = 0.0087

Table S41.  Gene #15: 'amp_16q12.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 15(16Q12.1) MUTATED 46 35 28
AMP PEAK 15(16Q12.1) WILD-TYPE 211 69 53

Figure S41.  Get High-res Image Gene #15: 'amp_16q12.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_16q12.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0146 (Fisher's exact test), Q value = 0.074

Table S42.  Gene #15: 'amp_16q12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 15(16Q12.1) MUTATED 101 7
AMP PEAK 15(16Q12.1) WILD-TYPE 280 53

Figure S42.  Get High-res Image Gene #15: 'amp_16q12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_16q12.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000328 (Wilcoxon-test), Q value = 0.0059

Table S43.  Gene #15: 'amp_16q12.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 15(16Q12.1) MUTATED 105 3.2 (6.2)
AMP PEAK 15(16Q12.1) WILD-TYPE 313 1.7 (3.6)

Figure S43.  Get High-res Image Gene #15: 'amp_16q12.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'amp_17q12' versus 'PATHOLOGY_M_STAGE'

P value = 0.0056 (Fisher's exact test), Q value = 0.04

Table S44.  Gene #17: 'amp_17q12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
AMP PEAK 17(17Q12) MUTATED 69 24
AMP PEAK 17(17Q12) WILD-TYPE 253 38

Figure S44.  Get High-res Image Gene #17: 'amp_17q12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_17q24.1' versus 'Time to Death'

P value = 0.0153 (logrank test), Q value = 0.076

Table S45.  Gene #18: 'amp_17q24.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
AMP PEAK 18(17Q24.1) MUTATED 101 12 0.1 - 130.7 (22.0)
AMP PEAK 18(17Q24.1) WILD-TYPE 329 81 0.0 - 140.4 (20.0)

Figure S45.  Get High-res Image Gene #18: 'amp_17q24.1' versus Clinical Feature #1: 'Time to Death'

'amp_19p13.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0505 (Fisher's exact test), Q value = 0.18

Table S46.  Gene #19: 'amp_19p13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 19(19P13.2) MUTATED 38 26 11
AMP PEAK 19(19P13.2) WILD-TYPE 219 78 70

Figure S46.  Get High-res Image Gene #19: 'amp_19p13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_20p12.1' versus 'Time to Death'

P value = 0.0723 (logrank test), Q value = 0.23

Table S47.  Gene #21: 'amp_20p12.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
AMP PEAK 21(20P12.1) MUTATED 200 48 0.0 - 139.2 (17.8)
AMP PEAK 21(20P12.1) WILD-TYPE 230 45 0.0 - 140.4 (23.3)

Figure S47.  Get High-res Image Gene #21: 'amp_20p12.1' versus Clinical Feature #1: 'Time to Death'

'amp_20p12.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00113 (Fisher's exact test), Q value = 0.012

Table S48.  Gene #21: 'amp_20p12.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
AMP PEAK 21(20P12.1) MUTATED 38 1 10 53 3 0 8 10 18 17 31 10 1
AMP PEAK 21(20P12.1) WILD-TYPE 36 0 18 78 5 1 13 2 38 22 12 8 1

Figure S48.  Get High-res Image Gene #21: 'amp_20p12.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_20p12.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.000752 (Fisher's exact test), Q value = 0.0099

Table S49.  Gene #21: 'amp_20p12.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
AMP PEAK 21(20P12.1) MUTATED 136 41
AMP PEAK 21(20P12.1) WILD-TYPE 186 21

Figure S49.  Get High-res Image Gene #21: 'amp_20p12.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_20p12.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0364 (Fisher's exact test), Q value = 0.14

Table S50.  Gene #21: 'amp_20p12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 21(20P12.1) MUTATED 184 20
AMP PEAK 21(20P12.1) WILD-TYPE 197 40

Figure S50.  Get High-res Image Gene #21: 'amp_20p12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_20p12.1' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0249 (Fisher's exact test), Q value = 0.11

Table S51.  Gene #21: 'amp_20p12.1' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
AMP PEAK 21(20P12.1) MUTATED 143 2 18 11
AMP PEAK 21(20P12.1) WILD-TYPE 173 1 6 14

Figure S51.  Get High-res Image Gene #21: 'amp_20p12.1' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'amp_20p11.21' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00179 (Fisher's exact test), Q value = 0.018

Table S52.  Gene #22: 'amp_20p11.21' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
AMP PEAK 22(20P11.21) MUTATED 43 1 14 65 3 0 9 11 26 21 35 12 1
AMP PEAK 22(20P11.21) WILD-TYPE 31 0 14 66 5 1 12 1 30 18 8 6 1

Figure S52.  Get High-res Image Gene #22: 'amp_20p11.21' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_20p11.21' versus 'PATHOLOGY_M_STAGE'

P value = 0.000435 (Fisher's exact test), Q value = 0.0071

Table S53.  Gene #22: 'amp_20p11.21' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
AMP PEAK 22(20P11.21) MUTATED 166 47
AMP PEAK 22(20P11.21) WILD-TYPE 156 15

Figure S53.  Get High-res Image Gene #22: 'amp_20p11.21' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_20p11.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00191 (Fisher's exact test), Q value = 0.019

Table S54.  Gene #22: 'amp_20p11.21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 22(20P11.21) MUTATED 224 22
AMP PEAK 22(20P11.21) WILD-TYPE 157 38

Figure S54.  Get High-res Image Gene #22: 'amp_20p11.21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_20p11.21' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0193 (Fisher's exact test), Q value = 0.09

Table S55.  Gene #22: 'amp_20p11.21' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
AMP PEAK 22(20P11.21) MUTATED 170 2 20 12
AMP PEAK 22(20P11.21) WILD-TYPE 146 1 4 13

Figure S55.  Get High-res Image Gene #22: 'amp_20p11.21' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'amp_20q11.21' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0025 (Fisher's exact test), Q value = 0.024

Table S56.  Gene #23: 'amp_20q11.21' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
AMP PEAK 23(20Q11.21) MUTATED 53 1 16 84 3 1 14 12 40 31 38 16 1
AMP PEAK 23(20Q11.21) WILD-TYPE 21 0 12 47 5 0 7 0 16 8 5 2 1

Figure S56.  Get High-res Image Gene #23: 'amp_20q11.21' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_20q11.21' versus 'PATHOLOGY_N_STAGE'

P value = 0.00623 (Fisher's exact test), Q value = 0.042

Table S57.  Gene #23: 'amp_20q11.21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 23(20Q11.21) MUTATED 169 84 63
AMP PEAK 23(20Q11.21) WILD-TYPE 88 20 18

Figure S57.  Get High-res Image Gene #23: 'amp_20q11.21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_20q11.21' versus 'PATHOLOGY_M_STAGE'

P value = 0.00316 (Fisher's exact test), Q value = 0.027

Table S58.  Gene #23: 'amp_20q11.21' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
AMP PEAK 23(20Q11.21) MUTATED 222 54
AMP PEAK 23(20Q11.21) WILD-TYPE 100 8

Figure S58.  Get High-res Image Gene #23: 'amp_20q11.21' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_20q11.21' versus 'HISTOLOGICAL_TYPE'

P value = 9.13e-07 (Fisher's exact test), Q value = 8.4e-05

Table S59.  Gene #23: 'amp_20q11.21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 23(20Q11.21) MUTATED 289 26
AMP PEAK 23(20Q11.21) WILD-TYPE 92 34

Figure S59.  Get High-res Image Gene #23: 'amp_20q11.21' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_20q11.21' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0127 (Wilcoxon-test), Q value = 0.066

Table S60.  Gene #23: 'amp_20q11.21' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 23(20Q11.21) MUTATED 303 2.3 (4.8)
AMP PEAK 23(20Q11.21) WILD-TYPE 115 1.5 (3.4)

Figure S60.  Get High-res Image Gene #23: 'amp_20q11.21' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'amp_20q12' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00099 (Fisher's exact test), Q value = 0.012

Table S61.  Gene #24: 'amp_20q12' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
AMP PEAK 24(20Q12) MUTATED 53 1 16 85 3 1 13 12 40 31 38 17 1
AMP PEAK 24(20Q12) WILD-TYPE 21 0 12 46 5 0 8 0 16 8 5 1 1

Figure S61.  Get High-res Image Gene #24: 'amp_20q12' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_20q12' versus 'PATHOLOGY_N_STAGE'

P value = 0.00846 (Fisher's exact test), Q value = 0.05

Table S62.  Gene #24: 'amp_20q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 24(20Q12) MUTATED 170 84 63
AMP PEAK 24(20Q12) WILD-TYPE 87 20 18

Figure S62.  Get High-res Image Gene #24: 'amp_20q12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_20q12' versus 'PATHOLOGY_M_STAGE'

P value = 0.00105 (Fisher's exact test), Q value = 0.012

Table S63.  Gene #24: 'amp_20q12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
AMP PEAK 24(20Q12) MUTATED 222 55
AMP PEAK 24(20Q12) WILD-TYPE 100 7

Figure S63.  Get High-res Image Gene #24: 'amp_20q12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_20q12' versus 'HISTOLOGICAL_TYPE'

P value = 1.52e-07 (Fisher's exact test), Q value = 3.1e-05

Table S64.  Gene #24: 'amp_20q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 24(20Q12) MUTATED 291 25
AMP PEAK 24(20Q12) WILD-TYPE 90 35

Figure S64.  Get High-res Image Gene #24: 'amp_20q12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_20q12' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0133 (Wilcoxon-test), Q value = 0.068

Table S65.  Gene #24: 'amp_20q12' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 24(20Q12) MUTATED 303 2.3 (4.8)
AMP PEAK 24(20Q12) WILD-TYPE 115 1.5 (3.5)

Figure S65.  Get High-res Image Gene #24: 'amp_20q12' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'amp_20q13.12' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00041 (Fisher's exact test), Q value = 0.0069

Table S66.  Gene #25: 'amp_20q13.12' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
AMP PEAK 25(20Q13.12) MUTATED 52 1 17 85 3 1 13 12 40 32 39 17 1
AMP PEAK 25(20Q13.12) WILD-TYPE 22 0 11 46 5 0 8 0 16 7 4 1 1

Figure S66.  Get High-res Image Gene #25: 'amp_20q13.12' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_20q13.12' versus 'PATHOLOGY_N_STAGE'

P value = 0.00414 (Fisher's exact test), Q value = 0.032

Table S67.  Gene #25: 'amp_20q13.12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
AMP PEAK 25(20Q13.12) MUTATED 170 84 65
AMP PEAK 25(20Q13.12) WILD-TYPE 87 20 16

Figure S67.  Get High-res Image Gene #25: 'amp_20q13.12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_20q13.12' versus 'PATHOLOGY_M_STAGE'

P value = 0.000505 (Fisher's exact test), Q value = 0.0076

Table S68.  Gene #25: 'amp_20q13.12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
AMP PEAK 25(20Q13.12) MUTATED 223 56
AMP PEAK 25(20Q13.12) WILD-TYPE 99 6

Figure S68.  Get High-res Image Gene #25: 'amp_20q13.12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_20q13.12' versus 'HISTOLOGICAL_TYPE'

P value = 6.1e-07 (Fisher's exact test), Q value = 8.4e-05

Table S69.  Gene #25: 'amp_20q13.12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
AMP PEAK 25(20Q13.12) MUTATED 292 26
AMP PEAK 25(20Q13.12) WILD-TYPE 89 34

Figure S69.  Get High-res Image Gene #25: 'amp_20q13.12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'amp_20q13.12' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00405 (Wilcoxon-test), Q value = 0.032

Table S70.  Gene #25: 'amp_20q13.12' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
AMP PEAK 25(20Q13.12) MUTATED 305 2.3 (4.8)
AMP PEAK 25(20Q13.12) WILD-TYPE 113 1.4 (3.3)

Figure S70.  Get High-res Image Gene #25: 'amp_20q13.12' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_1p36.11' versus 'Time to Death'

P value = 0.0457 (logrank test), Q value = 0.16

Table S71.  Gene #26: 'del_1p36.11' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
DEL PEAK 1(1P36.11) MUTATED 159 41 0.1 - 139.2 (19.1)
DEL PEAK 1(1P36.11) WILD-TYPE 271 52 0.0 - 140.4 (21.0)

Figure S71.  Get High-res Image Gene #26: 'del_1p36.11' versus Clinical Feature #1: 'Time to Death'

'del_1p36.11' versus 'YEARS_TO_BIRTH'

P value = 0.071 (Wilcoxon-test), Q value = 0.23

Table S72.  Gene #26: 'del_1p36.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 1(1P36.11) MUTATED 164 65.8 (12.2)
DEL PEAK 1(1P36.11) WILD-TYPE 277 67.6 (13.4)

Figure S72.  Get High-res Image Gene #26: 'del_1p36.11' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p36.11' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00068 (Fisher's exact test), Q value = 0.0091

Table S73.  Gene #26: 'del_1p36.11' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 1(1P36.11) MUTATED 21 0 5 45 1 1 8 4 19 17 29 10 0
DEL PEAK 1(1P36.11) WILD-TYPE 53 1 23 86 7 0 13 8 37 22 14 8 2

Figure S73.  Get High-res Image Gene #26: 'del_1p36.11' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_1p36.11' versus 'PATHOLOGY_N_STAGE'

P value = 0.00889 (Fisher's exact test), Q value = 0.051

Table S74.  Gene #26: 'del_1p36.11' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 1(1P36.11) MUTATED 81 43 40
DEL PEAK 1(1P36.11) WILD-TYPE 176 61 41

Figure S74.  Get High-res Image Gene #26: 'del_1p36.11' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p36.11' versus 'PATHOLOGY_M_STAGE'

P value = 1.35e-05 (Fisher's exact test), Q value = 0.00066

Table S75.  Gene #26: 'del_1p36.11' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 1(1P36.11) MUTATED 106 39
DEL PEAK 1(1P36.11) WILD-TYPE 216 23

Figure S75.  Get High-res Image Gene #26: 'del_1p36.11' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_1p36.11' versus 'HISTOLOGICAL_TYPE'

P value = 0.00138 (Fisher's exact test), Q value = 0.015

Table S76.  Gene #26: 'del_1p36.11' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 1(1P36.11) MUTATED 152 11
DEL PEAK 1(1P36.11) WILD-TYPE 229 49

Figure S76.  Get High-res Image Gene #26: 'del_1p36.11' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_1p36.11' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00256 (Wilcoxon-test), Q value = 0.024

Table S77.  Gene #26: 'del_1p36.11' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 1(1P36.11) MUTATED 153 2.9 (5.8)
DEL PEAK 1(1P36.11) WILD-TYPE 265 1.6 (3.4)

Figure S77.  Get High-res Image Gene #26: 'del_1p36.11' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_1p36.11' versus 'RACE'

P value = 0.0748 (Fisher's exact test), Q value = 0.23

Table S78.  Gene #26: 'del_1p36.11' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
DEL PEAK 1(1P36.11) MUTATED 1 7 16 79
DEL PEAK 1(1P36.11) WILD-TYPE 0 4 38 132

Figure S78.  Get High-res Image Gene #26: 'del_1p36.11' versus Clinical Feature #12: 'RACE'

'del_1p33' versus 'Time to Death'

P value = 0.00278 (logrank test), Q value = 0.025

Table S79.  Gene #27: 'del_1p33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
DEL PEAK 2(1P33) MUTATED 116 34 0.0 - 92.8 (17.9)
DEL PEAK 2(1P33) WILD-TYPE 314 59 0.0 - 140.4 (21.1)

Figure S79.  Get High-res Image Gene #27: 'del_1p33' versus Clinical Feature #1: 'Time to Death'

'del_1p33' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0155 (Fisher's exact test), Q value = 0.076

Table S80.  Gene #27: 'del_1p33' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 2(1P33) MUTATED 12 0 5 34 0 0 6 3 16 14 22 4 0
DEL PEAK 2(1P33) WILD-TYPE 62 1 23 97 8 1 15 9 40 25 21 14 2

Figure S80.  Get High-res Image Gene #27: 'del_1p33' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_1p33' versus 'PATHOLOGY_N_STAGE'

P value = 0.0155 (Fisher's exact test), Q value = 0.076

Table S81.  Gene #27: 'del_1p33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 2(1P33) MUTATED 57 33 30
DEL PEAK 2(1P33) WILD-TYPE 200 71 51

Figure S81.  Get High-res Image Gene #27: 'del_1p33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p33' versus 'PATHOLOGY_M_STAGE'

P value = 0.00473 (Fisher's exact test), Q value = 0.036

Table S82.  Gene #27: 'del_1p33' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 2(1P33) MUTATED 77 26
DEL PEAK 2(1P33) WILD-TYPE 245 36

Figure S82.  Get High-res Image Gene #27: 'del_1p33' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_1p33' versus 'HISTOLOGICAL_TYPE'

P value = 0.0602 (Fisher's exact test), Q value = 0.2

Table S83.  Gene #27: 'del_1p33' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 2(1P33) MUTATED 110 10
DEL PEAK 2(1P33) WILD-TYPE 271 50

Figure S83.  Get High-res Image Gene #27: 'del_1p33' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_1p33' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.005 (Wilcoxon-test), Q value = 0.036

Table S84.  Gene #27: 'del_1p33' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 2(1P33) MUTATED 113 3.2 (6.4)
DEL PEAK 2(1P33) WILD-TYPE 305 1.7 (3.4)

Figure S84.  Get High-res Image Gene #27: 'del_1p33' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_1p13.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00594 (Fisher's exact test), Q value = 0.041

Table S85.  Gene #28: 'del_1p13.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 3(1P13.1) MUTATED 12 0 5 31 0 0 5 3 16 13 23 3 0
DEL PEAK 3(1P13.1) WILD-TYPE 62 1 23 100 8 1 16 9 40 26 20 15 2

Figure S85.  Get High-res Image Gene #28: 'del_1p13.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_1p13.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0043 (Fisher's exact test), Q value = 0.033

Table S86.  Gene #28: 'del_1p13.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 3(1P13.1) MUTATED 53 31 31
DEL PEAK 3(1P13.1) WILD-TYPE 204 73 50

Figure S86.  Get High-res Image Gene #28: 'del_1p13.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p13.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.00267 (Fisher's exact test), Q value = 0.025

Table S87.  Gene #28: 'del_1p13.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 3(1P13.1) MUTATED 74 26
DEL PEAK 3(1P13.1) WILD-TYPE 248 36

Figure S87.  Get High-res Image Gene #28: 'del_1p13.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_1p13.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000557 (Wilcoxon-test), Q value = 0.008

Table S88.  Gene #28: 'del_1p13.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 3(1P13.1) MUTATED 106 3.0 (4.7)
DEL PEAK 3(1P13.1) WILD-TYPE 312 1.8 (4.3)

Figure S88.  Get High-res Image Gene #28: 'del_1p13.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_1q43' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0761 (Fisher's exact test), Q value = 0.24

Table S89.  Gene #29: 'del_1q43' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 4(1Q43) MUTATED 11 0 2 10 0 0 2 5 3 6 8 1 0
DEL PEAK 4(1Q43) WILD-TYPE 63 1 26 121 8 1 19 7 53 33 35 17 2

Figure S89.  Get High-res Image Gene #29: 'del_1q43' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_2q22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00925 (Wilcoxon-test), Q value = 0.052

Table S90.  Gene #31: 'del_2q22.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 6(2Q22.1) MUTATED 22 2.9 (3.2)
DEL PEAK 6(2Q22.1) WILD-TYPE 396 2.0 (4.5)

Figure S90.  Get High-res Image Gene #31: 'del_2q22.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_2q22.1' versus 'RACE'

P value = 0.00659 (Fisher's exact test), Q value = 0.042

Table S91.  Gene #31: 'del_2q22.1' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
DEL PEAK 6(2Q22.1) MUTATED 1 2 1 9
DEL PEAK 6(2Q22.1) WILD-TYPE 0 9 53 202

Figure S91.  Get High-res Image Gene #31: 'del_2q22.1' versus Clinical Feature #12: 'RACE'

'del_3p26.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0568 (Fisher's exact test), Q value = 0.19

Table S92.  Gene #32: 'del_3p26.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 7(3P26.2) MUTATED 6 0 1 19 0 0 4 2 11 8 14 4 0
DEL PEAK 7(3P26.2) WILD-TYPE 68 1 27 112 8 1 17 10 45 31 29 14 2

Figure S92.  Get High-res Image Gene #32: 'del_3p26.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_3p26.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00952 (Fisher's exact test), Q value = 0.053

Table S93.  Gene #32: 'del_3p26.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 7(3P26.2) MUTATED 29 21 19
DEL PEAK 7(3P26.2) WILD-TYPE 228 83 62

Figure S93.  Get High-res Image Gene #32: 'del_3p26.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_3p26.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.00347 (Fisher's exact test), Q value = 0.028

Table S94.  Gene #32: 'del_3p26.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 7(3P26.2) MUTATED 42 18
DEL PEAK 7(3P26.2) WILD-TYPE 280 44

Figure S94.  Get High-res Image Gene #32: 'del_3p26.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_3p26.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0367 (Fisher's exact test), Q value = 0.14

Table S95.  Gene #32: 'del_3p26.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 7(3P26.2) MUTATED 65 4
DEL PEAK 7(3P26.2) WILD-TYPE 316 56

Figure S95.  Get High-res Image Gene #32: 'del_3p26.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_3p26.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00616 (Wilcoxon-test), Q value = 0.042

Table S96.  Gene #32: 'del_3p26.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 7(3P26.2) MUTATED 65 3.2 (5.7)
DEL PEAK 7(3P26.2) WILD-TYPE 353 1.9 (4.2)

Figure S96.  Get High-res Image Gene #32: 'del_3p26.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_3p14.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0472 (Fisher's exact test), Q value = 0.17

Table S97.  Gene #33: 'del_3p14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 8(3P14.2) MUTATED 40 23 22
DEL PEAK 8(3P14.2) WILD-TYPE 217 81 59

Figure S97.  Get High-res Image Gene #33: 'del_3p14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_3p14.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0741 (Fisher's exact test), Q value = 0.23

Table S98.  Gene #33: 'del_3p14.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 8(3P14.2) MUTATED 55 17
DEL PEAK 8(3P14.2) WILD-TYPE 267 45

Figure S98.  Get High-res Image Gene #33: 'del_3p14.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_3p14.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0197 (Wilcoxon-test), Q value = 0.092

Table S99.  Gene #33: 'del_3p14.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 8(3P14.2) MUTATED 82 3.3 (6.0)
DEL PEAK 8(3P14.2) WILD-TYPE 336 1.8 (3.9)

Figure S99.  Get High-res Image Gene #33: 'del_3p14.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_4p16.2' versus 'Time to Death'

P value = 0.0134 (logrank test), Q value = 0.068

Table S100.  Gene #35: 'del_4p16.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
DEL PEAK 10(4P16.2) MUTATED 128 35 0.2 - 91.8 (20.2)
DEL PEAK 10(4P16.2) WILD-TYPE 302 58 0.0 - 140.4 (20.5)

Figure S100.  Get High-res Image Gene #35: 'del_4p16.2' versus Clinical Feature #1: 'Time to Death'

'del_4p16.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00084 (Fisher's exact test), Q value = 0.011

Table S101.  Gene #35: 'del_4p16.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 10(4P16.2) MUTATED 16 0 6 30 2 0 5 6 15 16 26 7 0
DEL PEAK 10(4P16.2) WILD-TYPE 58 1 22 101 6 1 16 6 41 23 17 11 2

Figure S101.  Get High-res Image Gene #35: 'del_4p16.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_4p16.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0042

Table S102.  Gene #35: 'del_4p16.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 10(4P16.2) MUTATED 58 39 36
DEL PEAK 10(4P16.2) WILD-TYPE 199 65 45

Figure S102.  Get High-res Image Gene #35: 'del_4p16.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_4p16.2' versus 'PATHOLOGY_M_STAGE'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.001

Table S103.  Gene #35: 'del_4p16.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 10(4P16.2) MUTATED 80 33
DEL PEAK 10(4P16.2) WILD-TYPE 242 29

Figure S103.  Get High-res Image Gene #35: 'del_4p16.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_4p16.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0346 (Fisher's exact test), Q value = 0.13

Table S104.  Gene #35: 'del_4p16.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 10(4P16.2) MUTATED 121 11
DEL PEAK 10(4P16.2) WILD-TYPE 260 49

Figure S104.  Get High-res Image Gene #35: 'del_4p16.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_4p16.2' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0266 (Fisher's exact test), Q value = 0.11

Table S105.  Gene #35: 'del_4p16.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
DEL PEAK 10(4P16.2) MUTATED 3 130
DEL PEAK 10(4P16.2) WILD-TYPE 0 310

Figure S105.  Get High-res Image Gene #35: 'del_4p16.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_4p16.2' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.034 (Fisher's exact test), Q value = 0.13

Table S106.  Gene #35: 'del_4p16.2' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
DEL PEAK 10(4P16.2) MUTATED 93 0 13 5
DEL PEAK 10(4P16.2) WILD-TYPE 223 3 11 20

Figure S106.  Get High-res Image Gene #35: 'del_4p16.2' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'del_4p16.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 8.63e-05 (Wilcoxon-test), Q value = 0.0022

Table S107.  Gene #35: 'del_4p16.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 10(4P16.2) MUTATED 128 3.0 (4.7)
DEL PEAK 10(4P16.2) WILD-TYPE 290 1.7 (4.3)

Figure S107.  Get High-res Image Gene #35: 'del_4p16.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_4q22.1' versus 'Time to Death'

P value = 0.028 (logrank test), Q value = 0.12

Table S108.  Gene #36: 'del_4q22.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
DEL PEAK 11(4Q22.1) MUTATED 142 38 0.0 - 102.4 (20.2)
DEL PEAK 11(4Q22.1) WILD-TYPE 288 55 0.0 - 140.4 (20.5)

Figure S108.  Get High-res Image Gene #36: 'del_4q22.1' versus Clinical Feature #1: 'Time to Death'

'del_4q22.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00272 (Fisher's exact test), Q value = 0.025

Table S109.  Gene #36: 'del_4q22.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 11(4Q22.1) MUTATED 14 0 8 37 2 0 3 7 23 19 21 6 1
DEL PEAK 11(4Q22.1) WILD-TYPE 60 1 20 94 6 1 18 5 33 20 22 12 1

Figure S109.  Get High-res Image Gene #36: 'del_4q22.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_4q22.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.0028

Table S110.  Gene #36: 'del_4q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 11(4Q22.1) MUTATED 64 44 37
DEL PEAK 11(4Q22.1) WILD-TYPE 193 60 44

Figure S110.  Get High-res Image Gene #36: 'del_4q22.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_4q22.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.017 (Fisher's exact test), Q value = 0.082

Table S111.  Gene #36: 'del_4q22.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 11(4Q22.1) MUTATED 94 28
DEL PEAK 11(4Q22.1) WILD-TYPE 228 34

Figure S111.  Get High-res Image Gene #36: 'del_4q22.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_4q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0115 (Fisher's exact test), Q value = 0.062

Table S112.  Gene #36: 'del_4q22.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 11(4Q22.1) MUTATED 133 11
DEL PEAK 11(4Q22.1) WILD-TYPE 248 49

Figure S112.  Get High-res Image Gene #36: 'del_4q22.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_4q22.1' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0346 (Fisher's exact test), Q value = 0.13

Table S113.  Gene #36: 'del_4q22.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
DEL PEAK 11(4Q22.1) MUTATED 3 142
DEL PEAK 11(4Q22.1) WILD-TYPE 0 298

Figure S113.  Get High-res Image Gene #36: 'del_4q22.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_4q22.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 7.86e-05 (Wilcoxon-test), Q value = 0.0022

Table S114.  Gene #36: 'del_4q22.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 11(4Q22.1) MUTATED 138 2.9 (4.6)
DEL PEAK 11(4Q22.1) WILD-TYPE 280 1.7 (4.4)

Figure S114.  Get High-res Image Gene #36: 'del_4q22.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_4q35.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0499 (Fisher's exact test), Q value = 0.17

Table S115.  Gene #37: 'del_4q35.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 12(4Q35.1) MUTATED 17 0 7 42 1 0 7 6 21 18 23 7 1
DEL PEAK 12(4Q35.1) WILD-TYPE 57 1 21 89 7 1 14 6 35 21 20 11 1

Figure S115.  Get High-res Image Gene #37: 'del_4q35.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_4q35.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00111 (Fisher's exact test), Q value = 0.012

Table S116.  Gene #37: 'del_4q35.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 12(4Q35.1) MUTATED 71 44 38
DEL PEAK 12(4Q35.1) WILD-TYPE 186 60 43

Figure S116.  Get High-res Image Gene #37: 'del_4q35.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_4q35.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.00857 (Fisher's exact test), Q value = 0.05

Table S117.  Gene #37: 'del_4q35.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 12(4Q35.1) MUTATED 103 31
DEL PEAK 12(4Q35.1) WILD-TYPE 219 31

Figure S117.  Get High-res Image Gene #37: 'del_4q35.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_4q35.1' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0407 (Fisher's exact test), Q value = 0.15

Table S118.  Gene #37: 'del_4q35.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
DEL PEAK 12(4Q35.1) MUTATED 3 150
DEL PEAK 12(4Q35.1) WILD-TYPE 0 290

Figure S118.  Get High-res Image Gene #37: 'del_4q35.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_4q35.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000314 (Wilcoxon-test), Q value = 0.0058

Table S119.  Gene #37: 'del_4q35.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 12(4Q35.1) MUTATED 146 2.7 (4.3)
DEL PEAK 12(4Q35.1) WILD-TYPE 272 1.8 (4.5)

Figure S119.  Get High-res Image Gene #37: 'del_4q35.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_5q12.1' versus 'YEARS_TO_BIRTH'

P value = 0.0667 (Wilcoxon-test), Q value = 0.22

Table S120.  Gene #38: 'del_5q12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 13(5Q12.1) MUTATED 103 65.2 (12.1)
DEL PEAK 13(5Q12.1) WILD-TYPE 338 67.5 (13.2)

Figure S120.  Get High-res Image Gene #38: 'del_5q12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5q12.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00792 (Fisher's exact test), Q value = 0.048

Table S121.  Gene #38: 'del_5q12.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 13(5Q12.1) MUTATED 17 0 4 18 1 0 4 6 13 15 12 8 1
DEL PEAK 13(5Q12.1) WILD-TYPE 57 1 24 113 7 1 17 6 43 24 31 10 1

Figure S121.  Get High-res Image Gene #38: 'del_5q12.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_5q12.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00926 (Fisher's exact test), Q value = 0.052

Table S122.  Gene #38: 'del_5q12.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 13(5Q12.1) MUTATED 47 29 27
DEL PEAK 13(5Q12.1) WILD-TYPE 210 75 54

Figure S122.  Get High-res Image Gene #38: 'del_5q12.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5q12.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.0294 (Fisher's exact test), Q value = 0.12

Table S123.  Gene #38: 'del_5q12.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 13(5Q12.1) MUTATED 65 21
DEL PEAK 13(5Q12.1) WILD-TYPE 257 41

Figure S123.  Get High-res Image Gene #38: 'del_5q12.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_5q12.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0498 (Fisher's exact test), Q value = 0.17

Table S124.  Gene #38: 'del_5q12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 13(5Q12.1) MUTATED 95 8
DEL PEAK 13(5Q12.1) WILD-TYPE 286 52

Figure S124.  Get High-res Image Gene #38: 'del_5q12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_5q12.1' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0123 (Fisher's exact test), Q value = 0.065

Table S125.  Gene #38: 'del_5q12.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
DEL PEAK 13(5Q12.1) MUTATED 3 100
DEL PEAK 13(5Q12.1) WILD-TYPE 0 340

Figure S125.  Get High-res Image Gene #38: 'del_5q12.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_5q12.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00339 (Wilcoxon-test), Q value = 0.028

Table S126.  Gene #38: 'del_5q12.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 13(5Q12.1) MUTATED 99 3.0 (5.1)
DEL PEAK 13(5Q12.1) WILD-TYPE 319 1.8 (4.2)

Figure S126.  Get High-res Image Gene #38: 'del_5q12.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_5q21.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 4e-04 (Fisher's exact test), Q value = 0.0069

Table S127.  Gene #39: 'del_5q21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 14(5Q21.1) MUTATED 18 0 5 25 0 0 4 8 17 17 16 8 2
DEL PEAK 14(5Q21.1) WILD-TYPE 56 1 23 106 8 1 17 4 39 22 27 10 0

Figure S127.  Get High-res Image Gene #39: 'del_5q21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_5q21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00109 (Fisher's exact test), Q value = 0.012

Table S128.  Gene #39: 'del_5q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 14(5Q21.1) MUTATED 55 37 32
DEL PEAK 14(5Q21.1) WILD-TYPE 202 67 49

Figure S128.  Get High-res Image Gene #39: 'del_5q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5q21.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.00812 (Fisher's exact test), Q value = 0.049

Table S129.  Gene #39: 'del_5q21.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 14(5Q21.1) MUTATED 80 26
DEL PEAK 14(5Q21.1) WILD-TYPE 242 36

Figure S129.  Get High-res Image Gene #39: 'del_5q21.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_5q21.1' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0215 (Fisher's exact test), Q value = 0.1

Table S130.  Gene #39: 'del_5q21.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
DEL PEAK 14(5Q21.1) MUTATED 3 121
DEL PEAK 14(5Q21.1) WILD-TYPE 0 319

Figure S130.  Get High-res Image Gene #39: 'del_5q21.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_5q21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000264 (Wilcoxon-test), Q value = 0.005

Table S131.  Gene #39: 'del_5q21.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 14(5Q21.1) MUTATED 119 3.0 (4.9)
DEL PEAK 14(5Q21.1) WILD-TYPE 299 1.7 (4.2)

Figure S131.  Get High-res Image Gene #39: 'del_5q21.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_5q22.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.024 (Fisher's exact test), Q value = 0.11

Table S132.  Gene #40: 'del_5q22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 15(5Q22.2) MUTATED 19 0 6 28 0 0 5 7 15 15 18 8 1
DEL PEAK 15(5Q22.2) WILD-TYPE 55 1 22 103 8 1 16 5 41 24 25 10 1

Figure S132.  Get High-res Image Gene #40: 'del_5q22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_5q22.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0285 (Fisher's exact test), Q value = 0.12

Table S133.  Gene #40: 'del_5q22.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 15(5Q22.2) MUTATED 62 34 31
DEL PEAK 15(5Q22.2) WILD-TYPE 195 70 50

Figure S133.  Get High-res Image Gene #40: 'del_5q22.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5q22.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.00312 (Fisher's exact test), Q value = 0.027

Table S134.  Gene #40: 'del_5q22.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 15(5Q22.2) MUTATED 79 27
DEL PEAK 15(5Q22.2) WILD-TYPE 243 35

Figure S134.  Get High-res Image Gene #40: 'del_5q22.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_5q22.2' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0232 (Fisher's exact test), Q value = 0.1

Table S135.  Gene #40: 'del_5q22.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
DEL PEAK 15(5Q22.2) MUTATED 3 124
DEL PEAK 15(5Q22.2) WILD-TYPE 0 316

Figure S135.  Get High-res Image Gene #40: 'del_5q22.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_5q22.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0117 (Wilcoxon-test), Q value = 0.062

Table S136.  Gene #40: 'del_5q22.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 15(5Q22.2) MUTATED 120 2.8 (4.8)
DEL PEAK 15(5Q22.2) WILD-TYPE 298 1.8 (4.3)

Figure S136.  Get High-res Image Gene #40: 'del_5q22.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_6p25.3' versus 'YEARS_TO_BIRTH'

P value = 0.0759 (Wilcoxon-test), Q value = 0.24

Table S137.  Gene #41: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 16(6P25.3) MUTATED 54 69.6 (12.7)
DEL PEAK 16(6P25.3) WILD-TYPE 387 66.6 (13.0)

Figure S137.  Get High-res Image Gene #41: 'del_6p25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6p25.3' versus 'GENDER'

P value = 0.0596 (Fisher's exact test), Q value = 0.2

Table S138.  Gene #41: 'del_6p25.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 210 233
DEL PEAK 16(6P25.3) MUTATED 19 35
DEL PEAK 16(6P25.3) WILD-TYPE 191 198

Figure S138.  Get High-res Image Gene #41: 'del_6p25.3' versus Clinical Feature #7: 'GENDER'

'del_6p25.3' versus 'RACE'

P value = 0.0154 (Fisher's exact test), Q value = 0.076

Table S139.  Gene #41: 'del_6p25.3' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
DEL PEAK 16(6P25.3) MUTATED 0 3 1 26
DEL PEAK 16(6P25.3) WILD-TYPE 1 8 53 185

Figure S139.  Get High-res Image Gene #41: 'del_6p25.3' versus Clinical Feature #12: 'RACE'

'del_6q26' versus 'Time to Death'

P value = 0.0185 (logrank test), Q value = 0.088

Table S140.  Gene #42: 'del_6q26' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
DEL PEAK 17(6Q26) MUTATED 59 19 0.2 - 131.5 (17.8)
DEL PEAK 17(6Q26) WILD-TYPE 371 74 0.0 - 140.4 (21.4)

Figure S140.  Get High-res Image Gene #42: 'del_6q26' versus Clinical Feature #1: 'Time to Death'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.00285 (Fisher's exact test), Q value = 0.025

Table S141.  Gene #42: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 17(6Q26) MUTATED 26 14 21
DEL PEAK 17(6Q26) WILD-TYPE 231 90 60

Figure S141.  Get High-res Image Gene #42: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'PATHOLOGY_M_STAGE'

P value = 0.0245 (Fisher's exact test), Q value = 0.11

Table S142.  Gene #42: 'del_6q26' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 17(6Q26) MUTATED 37 14
DEL PEAK 17(6Q26) WILD-TYPE 285 48

Figure S142.  Get High-res Image Gene #42: 'del_6q26' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_6q26' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00105 (Wilcoxon-test), Q value = 0.012

Table S143.  Gene #42: 'del_6q26' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 17(6Q26) MUTATED 57 3.5 (4.6)
DEL PEAK 17(6Q26) WILD-TYPE 361 1.9 (4.4)

Figure S143.  Get High-res Image Gene #42: 'del_6q26' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_6q26' versus 'RACE'

P value = 0.053 (Fisher's exact test), Q value = 0.18

Table S144.  Gene #42: 'del_6q26' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
DEL PEAK 17(6Q26) MUTATED 1 3 5 26
DEL PEAK 17(6Q26) WILD-TYPE 0 8 49 185

Figure S144.  Get High-res Image Gene #42: 'del_6q26' versus Clinical Feature #12: 'RACE'

'del_8p23.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00112 (Fisher's exact test), Q value = 0.012

Table S145.  Gene #44: 'del_8p23.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 19(8P23.3) MUTATED 25 0 8 41 2 0 10 6 28 23 28 10 1
DEL PEAK 19(8P23.3) WILD-TYPE 49 1 20 90 6 1 11 6 28 16 15 8 1

Figure S145.  Get High-res Image Gene #44: 'del_8p23.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_8p23.3' versus 'PATHOLOGY_N_STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0022

Table S146.  Gene #44: 'del_8p23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 19(8P23.3) MUTATED 85 51 48
DEL PEAK 19(8P23.3) WILD-TYPE 172 53 33

Figure S146.  Get High-res Image Gene #44: 'del_8p23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_8p23.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.000438 (Fisher's exact test), Q value = 0.0071

Table S147.  Gene #44: 'del_8p23.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 19(8P23.3) MUTATED 124 39
DEL PEAK 19(8P23.3) WILD-TYPE 198 23

Figure S147.  Get High-res Image Gene #44: 'del_8p23.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_8p23.3' versus 'GENDER'

P value = 0.0159 (Fisher's exact test), Q value = 0.077

Table S148.  Gene #44: 'del_8p23.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 210 233
DEL PEAK 19(8P23.3) MUTATED 75 110
DEL PEAK 19(8P23.3) WILD-TYPE 135 123

Figure S148.  Get High-res Image Gene #44: 'del_8p23.3' versus Clinical Feature #7: 'GENDER'

'del_8p23.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0246 (Fisher's exact test), Q value = 0.11

Table S149.  Gene #44: 'del_8p23.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 19(8P23.3) MUTATED 167 17
DEL PEAK 19(8P23.3) WILD-TYPE 214 43

Figure S149.  Get High-res Image Gene #44: 'del_8p23.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_8p23.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 4.19e-05 (Wilcoxon-test), Q value = 0.0014

Table S150.  Gene #44: 'del_8p23.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 19(8P23.3) MUTATED 178 2.9 (5.5)
DEL PEAK 19(8P23.3) WILD-TYPE 240 1.5 (3.3)

Figure S150.  Get High-res Image Gene #44: 'del_8p23.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_8p22' versus 'YEARS_TO_BIRTH'

P value = 0.0318 (Wilcoxon-test), Q value = 0.13

Table S151.  Gene #45: 'del_8p22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 20(8P22) MUTATED 199 65.7 (12.1)
DEL PEAK 20(8P22) WILD-TYPE 242 67.9 (13.6)

Figure S151.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_8p22' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00052

Table S152.  Gene #45: 'del_8p22' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 20(8P22) MUTATED 25 0 9 42 2 0 10 8 31 25 29 14 1
DEL PEAK 20(8P22) WILD-TYPE 49 1 19 89 6 1 11 4 25 14 14 4 1

Figure S152.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_8p22' versus 'PATHOLOGY_T_STAGE'

P value = 0.053 (Fisher's exact test), Q value = 0.18

Table S153.  Gene #45: 'del_8p22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 11 78 301 52
DEL PEAK 20(8P22) MUTATED 1 31 142 25
DEL PEAK 20(8P22) WILD-TYPE 10 47 159 27

Figure S153.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_8p22' versus 'PATHOLOGY_N_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00052

Table S154.  Gene #45: 'del_8p22' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 20(8P22) MUTATED 89 55 54
DEL PEAK 20(8P22) WILD-TYPE 168 49 27

Figure S154.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_8p22' versus 'PATHOLOGY_M_STAGE'

P value = 2.17e-05 (Fisher's exact test), Q value = 0.00092

Table S155.  Gene #45: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 20(8P22) MUTATED 132 44
DEL PEAK 20(8P22) WILD-TYPE 190 18

Figure S155.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_8p22' versus 'GENDER'

P value = 0.0558 (Fisher's exact test), Q value = 0.19

Table S156.  Gene #45: 'del_8p22' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 210 233
DEL PEAK 20(8P22) MUTATED 84 115
DEL PEAK 20(8P22) WILD-TYPE 126 118

Figure S156.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #7: 'GENDER'

'del_8p22' versus 'HISTOLOGICAL_TYPE'

P value = 0.00758 (Fisher's exact test), Q value = 0.047

Table S157.  Gene #45: 'del_8p22' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 20(8P22) MUTATED 181 17
DEL PEAK 20(8P22) WILD-TYPE 200 43

Figure S157.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_8p22' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0403 (Fisher's exact test), Q value = 0.15

Table S158.  Gene #45: 'del_8p22' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
DEL PEAK 20(8P22) MUTATED 138 1 15 6
DEL PEAK 20(8P22) WILD-TYPE 178 2 9 19

Figure S158.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'del_8p22' versus 'NUMBER_OF_LYMPH_NODES'

P value = 7.4e-07 (Wilcoxon-test), Q value = 8.4e-05

Table S159.  Gene #45: 'del_8p22' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 20(8P22) MUTATED 192 2.9 (5.4)
DEL PEAK 20(8P22) WILD-TYPE 226 1.4 (3.3)

Figure S159.  Get High-res Image Gene #45: 'del_8p22' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_8q11.1' versus 'RACE'

P value = 0.0467 (Fisher's exact test), Q value = 0.17

Table S160.  Gene #46: 'del_8q11.1' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
DEL PEAK 21(8Q11.1) MUTATED 1 0 6 13
DEL PEAK 21(8Q11.1) WILD-TYPE 0 11 48 198

Figure S160.  Get High-res Image Gene #46: 'del_8q11.1' versus Clinical Feature #12: 'RACE'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 0.0359 (Wilcoxon-test), Q value = 0.14

Table S161.  Gene #47: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 22(9P21.3) MUTATED 59 63.8 (12.7)
DEL PEAK 22(9P21.3) WILD-TYPE 382 67.4 (13.0)

Figure S161.  Get High-res Image Gene #47: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.041 (Fisher's exact test), Q value = 0.15

Table S162.  Gene #47: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 22(9P21.3) MUTATED 56 3
DEL PEAK 22(9P21.3) WILD-TYPE 325 57

Figure S162.  Get High-res Image Gene #47: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_10p15.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0014 (Fisher's exact test), Q value = 0.015

Table S163.  Gene #48: 'del_10p15.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 23(10P15.3) MUTATED 10 0 6 12 0 1 2 4 11 8 16 4 1
DEL PEAK 23(10P15.3) WILD-TYPE 64 1 22 119 8 0 19 8 45 31 27 14 1

Figure S163.  Get High-res Image Gene #48: 'del_10p15.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_10p15.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00927 (Fisher's exact test), Q value = 0.052

Table S164.  Gene #48: 'del_10p15.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 23(10P15.3) MUTATED 33 23 21
DEL PEAK 23(10P15.3) WILD-TYPE 224 81 60

Figure S164.  Get High-res Image Gene #48: 'del_10p15.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_10p15.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.000814 (Fisher's exact test), Q value = 0.011

Table S165.  Gene #48: 'del_10p15.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 23(10P15.3) MUTATED 47 21
DEL PEAK 23(10P15.3) WILD-TYPE 275 41

Figure S165.  Get High-res Image Gene #48: 'del_10p15.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_10p15.3' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0795 (Fisher's exact test), Q value = 0.25

Table S166.  Gene #48: 'del_10p15.3' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
DEL PEAK 23(10P15.3) MUTATED 2 75
DEL PEAK 23(10P15.3) WILD-TYPE 1 365

Figure S166.  Get High-res Image Gene #48: 'del_10p15.3' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_10p15.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0026 (Wilcoxon-test), Q value = 0.024

Table S167.  Gene #48: 'del_10p15.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 23(10P15.3) MUTATED 74 3.1 (6.4)
DEL PEAK 23(10P15.3) WILD-TYPE 344 1.9 (3.9)

Figure S167.  Get High-res Image Gene #48: 'del_10p15.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_10q21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0421 (Wilcoxon-test), Q value = 0.15

Table S168.  Gene #49: 'del_10q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 24(10Q21.1) MUTATED 94 64.4 (13.3)
DEL PEAK 24(10Q21.1) WILD-TYPE 347 67.6 (12.9)

Figure S168.  Get High-res Image Gene #49: 'del_10q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q21.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00581 (Fisher's exact test), Q value = 0.041

Table S169.  Gene #49: 'del_10q21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 24(10Q21.1) MUTATED 12 0 6 18 0 1 2 3 13 14 16 5 1
DEL PEAK 24(10Q21.1) WILD-TYPE 62 1 22 113 8 0 19 9 43 25 27 13 1

Figure S169.  Get High-res Image Gene #49: 'del_10q21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_10q21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00979 (Fisher's exact test), Q value = 0.054

Table S170.  Gene #49: 'del_10q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 24(10Q21.1) MUTATED 43 25 26
DEL PEAK 24(10Q21.1) WILD-TYPE 214 79 55

Figure S170.  Get High-res Image Gene #49: 'del_10q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_10q21.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.00646 (Fisher's exact test), Q value = 0.042

Table S171.  Gene #49: 'del_10q21.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 24(10Q21.1) MUTATED 61 22
DEL PEAK 24(10Q21.1) WILD-TYPE 261 40

Figure S171.  Get High-res Image Gene #49: 'del_10q21.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_10q21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.061 (Fisher's exact test), Q value = 0.2

Table S172.  Gene #49: 'del_10q21.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 24(10Q21.1) MUTATED 87 7
DEL PEAK 24(10Q21.1) WILD-TYPE 294 53

Figure S172.  Get High-res Image Gene #49: 'del_10q21.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_10q21.1' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0661 (Fisher's exact test), Q value = 0.22

Table S173.  Gene #49: 'del_10q21.1' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
DEL PEAK 24(10Q21.1) MUTATED 63 1 10 6
DEL PEAK 24(10Q21.1) WILD-TYPE 253 2 14 19

Figure S173.  Get High-res Image Gene #49: 'del_10q21.1' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'del_10q21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00401 (Wilcoxon-test), Q value = 0.032

Table S174.  Gene #49: 'del_10q21.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 24(10Q21.1) MUTATED 90 3.0 (6.2)
DEL PEAK 24(10Q21.1) WILD-TYPE 328 1.8 (3.8)

Figure S174.  Get High-res Image Gene #49: 'del_10q21.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 0.00371 (Wilcoxon-test), Q value = 0.03

Table S175.  Gene #50: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 25(10Q23.31) MUTATED 106 63.8 (13.0)
DEL PEAK 25(10Q23.31) WILD-TYPE 335 68.0 (12.9)

Figure S175.  Get High-res Image Gene #50: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00316 (Fisher's exact test), Q value = 0.027

Table S176.  Gene #50: 'del_10q23.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 25(10Q23.31) MUTATED 14 1 6 23 0 1 4 6 13 12 17 5 2
DEL PEAK 25(10Q23.31) WILD-TYPE 60 0 22 108 8 0 17 6 43 27 26 13 0

Figure S176.  Get High-res Image Gene #50: 'del_10q23.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_10q23.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.0263 (Fisher's exact test), Q value = 0.11

Table S177.  Gene #50: 'del_10q23.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 25(10Q23.31) MUTATED 50 30 26
DEL PEAK 25(10Q23.31) WILD-TYPE 207 74 55

Figure S177.  Get High-res Image Gene #50: 'del_10q23.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_10q23.31' versus 'PATHOLOGY_M_STAGE'

P value = 0.00944 (Fisher's exact test), Q value = 0.053

Table S178.  Gene #50: 'del_10q23.31' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 25(10Q23.31) MUTATED 71 24
DEL PEAK 25(10Q23.31) WILD-TYPE 251 38

Figure S178.  Get High-res Image Gene #50: 'del_10q23.31' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_10q23.31' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00526 (Wilcoxon-test), Q value = 0.038

Table S179.  Gene #50: 'del_10q23.31' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 25(10Q23.31) MUTATED 102 2.5 (3.8)
DEL PEAK 25(10Q23.31) WILD-TYPE 316 2.0 (4.6)

Figure S179.  Get High-res Image Gene #50: 'del_10q23.31' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_10q25.2' versus 'YEARS_TO_BIRTH'

P value = 0.0663 (Wilcoxon-test), Q value = 0.22

Table S180.  Gene #51: 'del_10q25.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 26(10Q25.2) MUTATED 106 65.0 (12.9)
DEL PEAK 26(10Q25.2) WILD-TYPE 335 67.6 (13.0)

Figure S180.  Get High-res Image Gene #51: 'del_10q25.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q25.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0295 (Fisher's exact test), Q value = 0.12

Table S181.  Gene #51: 'del_10q25.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 26(10Q25.2) MUTATED 11 0 7 25 0 1 6 4 13 12 18 5 1
DEL PEAK 26(10Q25.2) WILD-TYPE 63 1 21 106 8 0 15 8 43 27 25 13 1

Figure S181.  Get High-res Image Gene #51: 'del_10q25.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_10q25.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00774 (Fisher's exact test), Q value = 0.047

Table S182.  Gene #51: 'del_10q25.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 26(10Q25.2) MUTATED 48 31 27
DEL PEAK 26(10Q25.2) WILD-TYPE 209 73 54

Figure S182.  Get High-res Image Gene #51: 'del_10q25.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_10q25.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.00986 (Fisher's exact test), Q value = 0.054

Table S183.  Gene #51: 'del_10q25.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 26(10Q25.2) MUTATED 72 24
DEL PEAK 26(10Q25.2) WILD-TYPE 250 38

Figure S183.  Get High-res Image Gene #51: 'del_10q25.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_10q25.2' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.0751 (Fisher's exact test), Q value = 0.23

Table S184.  Gene #51: 'del_10q25.2' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
DEL PEAK 26(10Q25.2) MUTATED 72 1 11 5
DEL PEAK 26(10Q25.2) WILD-TYPE 244 2 13 20

Figure S184.  Get High-res Image Gene #51: 'del_10q25.2' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'del_10q25.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00383 (Wilcoxon-test), Q value = 0.031

Table S185.  Gene #51: 'del_10q25.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 26(10Q25.2) MUTATED 102 2.6 (3.9)
DEL PEAK 26(10Q25.2) WILD-TYPE 316 1.9 (4.6)

Figure S185.  Get High-res Image Gene #51: 'del_10q25.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_12p13.2' versus 'Time to Death'

P value = 0.0231 (logrank test), Q value = 0.1

Table S186.  Gene #52: 'del_12p13.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
DEL PEAK 27(12P13.2) MUTATED 59 18 0.1 - 78.1 (16.2)
DEL PEAK 27(12P13.2) WILD-TYPE 371 75 0.0 - 140.4 (21.1)

Figure S186.  Get High-res Image Gene #52: 'del_12p13.2' versus Clinical Feature #1: 'Time to Death'

'del_12p13.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0583 (Fisher's exact test), Q value = 0.19

Table S187.  Gene #52: 'del_12p13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 27(12P13.2) MUTATED 26 19 14
DEL PEAK 27(12P13.2) WILD-TYPE 231 85 67

Figure S187.  Get High-res Image Gene #52: 'del_12p13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_12p13.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0357 (Fisher's exact test), Q value = 0.14

Table S188.  Gene #52: 'del_12p13.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 27(12P13.2) MUTATED 35 13
DEL PEAK 27(12P13.2) WILD-TYPE 287 49

Figure S188.  Get High-res Image Gene #52: 'del_12p13.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_12p13.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0128 (Fisher's exact test), Q value = 0.066

Table S189.  Gene #52: 'del_12p13.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 27(12P13.2) MUTATED 57 2
DEL PEAK 27(12P13.2) WILD-TYPE 324 58

Figure S189.  Get High-res Image Gene #52: 'del_12p13.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_12p13.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0668 (Wilcoxon-test), Q value = 0.22

Table S190.  Gene #52: 'del_12p13.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 27(12P13.2) MUTATED 55 2.3 (3.5)
DEL PEAK 27(12P13.2) WILD-TYPE 363 2.1 (4.6)

Figure S190.  Get High-res Image Gene #52: 'del_12p13.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_13q14.13' versus 'PATHOLOGY_N_STAGE'

P value = 0.0344 (Fisher's exact test), Q value = 0.13

Table S191.  Gene #53: 'del_13q14.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 28(13Q14.13) MUTATED 11 1 7
DEL PEAK 28(13Q14.13) WILD-TYPE 246 103 74

Figure S191.  Get High-res Image Gene #53: 'del_13q14.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_13q14.13' versus 'RACE'

P value = 0.0366 (Fisher's exact test), Q value = 0.14

Table S192.  Gene #53: 'del_13q14.13' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 54 211
DEL PEAK 28(13Q14.13) MUTATED 1 1 3 8
DEL PEAK 28(13Q14.13) WILD-TYPE 0 10 51 203

Figure S192.  Get High-res Image Gene #53: 'del_13q14.13' versus Clinical Feature #12: 'RACE'

'del_14q31.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0233 (Fisher's exact test), Q value = 0.1

Table S193.  Gene #54: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 29(14Q31.1) MUTATED 71 41 33
DEL PEAK 29(14Q31.1) WILD-TYPE 186 63 48

Figure S193.  Get High-res Image Gene #54: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_14q31.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.00491 (Fisher's exact test), Q value = 0.036

Table S194.  Gene #54: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 29(14Q31.1) MUTATED 98 31
DEL PEAK 29(14Q31.1) WILD-TYPE 224 31

Figure S194.  Get High-res Image Gene #54: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_14q31.1' versus 'HISTOLOGICAL_TYPE'

P value = 5.09e-06 (Fisher's exact test), Q value = 0.00033

Table S195.  Gene #54: 'del_14q31.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 29(14Q31.1) MUTATED 138 5
DEL PEAK 29(14Q31.1) WILD-TYPE 243 55

Figure S195.  Get High-res Image Gene #54: 'del_14q31.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_14q31.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0128 (Wilcoxon-test), Q value = 0.066

Table S196.  Gene #54: 'del_14q31.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 29(14Q31.1) MUTATED 137 2.6 (4.9)
DEL PEAK 29(14Q31.1) WILD-TYPE 281 1.8 (4.2)

Figure S196.  Get High-res Image Gene #54: 'del_14q31.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_15q11.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.01 (Fisher's exact test), Q value = 0.054

Table S197.  Gene #55: 'del_15q11.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 30(15Q11.2) MUTATED 28 0 7 40 2 0 6 8 23 20 22 11 2
DEL PEAK 30(15Q11.2) WILD-TYPE 46 1 21 91 6 1 15 4 33 19 21 7 0

Figure S197.  Get High-res Image Gene #55: 'del_15q11.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_15q11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00873 (Fisher's exact test), Q value = 0.051

Table S198.  Gene #55: 'del_15q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 30(15Q11.2) MUTATED 85 49 39
DEL PEAK 30(15Q11.2) WILD-TYPE 172 55 42

Figure S198.  Get High-res Image Gene #55: 'del_15q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_15q11.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.00422 (Fisher's exact test), Q value = 0.032

Table S199.  Gene #55: 'del_15q11.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 30(15Q11.2) MUTATED 116 35
DEL PEAK 30(15Q11.2) WILD-TYPE 206 27

Figure S199.  Get High-res Image Gene #55: 'del_15q11.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_15q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0456 (Fisher's exact test), Q value = 0.16

Table S200.  Gene #55: 'del_15q11.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 30(15Q11.2) MUTATED 155 16
DEL PEAK 30(15Q11.2) WILD-TYPE 226 44

Figure S200.  Get High-res Image Gene #55: 'del_15q11.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_15q11.2' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0589 (Fisher's exact test), Q value = 0.2

Table S201.  Gene #55: 'del_15q11.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
DEL PEAK 30(15Q11.2) MUTATED 3 170
DEL PEAK 30(15Q11.2) WILD-TYPE 0 270

Figure S201.  Get High-res Image Gene #55: 'del_15q11.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_15q11.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00493 (Wilcoxon-test), Q value = 0.036

Table S202.  Gene #55: 'del_15q11.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 30(15Q11.2) MUTATED 165 2.4 (3.8)
DEL PEAK 30(15Q11.2) WILD-TYPE 253 1.9 (4.8)

Figure S202.  Get High-res Image Gene #55: 'del_15q11.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_15q15.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0138 (Fisher's exact test), Q value = 0.07

Table S203.  Gene #56: 'del_15q15.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 31(15Q15.2) MUTATED 29 0 7 37 2 0 6 6 22 19 24 10 2
DEL PEAK 31(15Q15.2) WILD-TYPE 45 1 21 94 6 1 15 6 34 20 19 8 0

Figure S203.  Get High-res Image Gene #56: 'del_15q15.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_15q15.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00649 (Fisher's exact test), Q value = 0.042

Table S204.  Gene #56: 'del_15q15.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 31(15Q15.2) MUTATED 82 50 36
DEL PEAK 31(15Q15.2) WILD-TYPE 175 54 45

Figure S204.  Get High-res Image Gene #56: 'del_15q15.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_15q15.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.000501 (Fisher's exact test), Q value = 0.0076

Table S205.  Gene #56: 'del_15q15.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 31(15Q15.2) MUTATED 108 36
DEL PEAK 31(15Q15.2) WILD-TYPE 214 26

Figure S205.  Get High-res Image Gene #56: 'del_15q15.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_15q15.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.0317 (Fisher's exact test), Q value = 0.13

Table S206.  Gene #56: 'del_15q15.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 31(15Q15.2) MUTATED 151 15
DEL PEAK 31(15Q15.2) WILD-TYPE 230 45

Figure S206.  Get High-res Image Gene #56: 'del_15q15.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_15q15.2' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0539 (Fisher's exact test), Q value = 0.18

Table S207.  Gene #56: 'del_15q15.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
DEL PEAK 31(15Q15.2) MUTATED 3 165
DEL PEAK 31(15Q15.2) WILD-TYPE 0 275

Figure S207.  Get High-res Image Gene #56: 'del_15q15.2' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_15q15.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00929 (Wilcoxon-test), Q value = 0.052

Table S208.  Gene #56: 'del_15q15.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 31(15Q15.2) MUTATED 161 2.3 (3.8)
DEL PEAK 31(15Q15.2) WILD-TYPE 257 1.9 (4.8)

Figure S208.  Get High-res Image Gene #56: 'del_15q15.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_15q21.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0692 (Fisher's exact test), Q value = 0.22

Table S209.  Gene #57: 'del_15q21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 32(15Q21.1) MUTATED 26 0 7 40 3 0 6 6 20 18 23 10 2
DEL PEAK 32(15Q21.1) WILD-TYPE 48 1 21 91 5 1 15 6 36 21 20 8 0

Figure S209.  Get High-res Image Gene #57: 'del_15q21.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_15q21.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0336 (Fisher's exact test), Q value = 0.13

Table S210.  Gene #57: 'del_15q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 32(15Q21.1) MUTATED 83 47 35
DEL PEAK 32(15Q21.1) WILD-TYPE 174 57 46

Figure S210.  Get High-res Image Gene #57: 'del_15q21.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_15q21.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.000847 (Fisher's exact test), Q value = 0.011

Table S211.  Gene #57: 'del_15q21.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 32(15Q21.1) MUTATED 107 35
DEL PEAK 32(15Q21.1) WILD-TYPE 215 27

Figure S211.  Get High-res Image Gene #57: 'del_15q21.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_15q21.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0437 (Fisher's exact test), Q value = 0.16

Table S212.  Gene #57: 'del_15q21.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 32(15Q21.1) MUTATED 149 15
DEL PEAK 32(15Q21.1) WILD-TYPE 232 45

Figure S212.  Get High-res Image Gene #57: 'del_15q21.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_15q21.1' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.0511 (Fisher's exact test), Q value = 0.18

Table S213.  Gene #57: 'del_15q21.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
DEL PEAK 32(15Q21.1) MUTATED 3 162
DEL PEAK 32(15Q21.1) WILD-TYPE 0 278

Figure S213.  Get High-res Image Gene #57: 'del_15q21.1' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_15q21.1' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0349 (Wilcoxon-test), Q value = 0.13

Table S214.  Gene #57: 'del_15q21.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 32(15Q21.1) MUTATED 158 2.3 (3.8)
DEL PEAK 32(15Q21.1) WILD-TYPE 260 2.0 (4.8)

Figure S214.  Get High-res Image Gene #57: 'del_15q21.1' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_15q22.33' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00679 (Fisher's exact test), Q value = 0.043

Table S215.  Gene #58: 'del_15q22.33' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 33(15Q22.33) MUTATED 23 0 6 37 2 0 5 7 19 20 22 11 1
DEL PEAK 33(15Q22.33) WILD-TYPE 51 1 22 94 6 1 16 5 37 19 21 7 1

Figure S215.  Get High-res Image Gene #58: 'del_15q22.33' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_15q22.33' versus 'PATHOLOGY_N_STAGE'

P value = 0.00725 (Fisher's exact test), Q value = 0.045

Table S216.  Gene #58: 'del_15q22.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 33(15Q22.33) MUTATED 76 44 37
DEL PEAK 33(15Q22.33) WILD-TYPE 181 60 44

Figure S216.  Get High-res Image Gene #58: 'del_15q22.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_15q22.33' versus 'PATHOLOGY_M_STAGE'

P value = 0.000456 (Fisher's exact test), Q value = 0.0073

Table S217.  Gene #58: 'del_15q22.33' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 33(15Q22.33) MUTATED 100 34
DEL PEAK 33(15Q22.33) WILD-TYPE 222 28

Figure S217.  Get High-res Image Gene #58: 'del_15q22.33' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_15q22.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.0421 (Fisher's exact test), Q value = 0.15

Table S218.  Gene #58: 'del_15q22.33' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 33(15Q22.33) MUTATED 141 14
DEL PEAK 33(15Q22.33) WILD-TYPE 240 46

Figure S218.  Get High-res Image Gene #58: 'del_15q22.33' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_15q22.33' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.044 (Fisher's exact test), Q value = 0.16

Table S219.  Gene #58: 'del_15q22.33' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 440
DEL PEAK 33(15Q22.33) MUTATED 3 154
DEL PEAK 33(15Q22.33) WILD-TYPE 0 286

Figure S219.  Get High-res Image Gene #58: 'del_15q22.33' versus Clinical Feature #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'del_15q22.33' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00617 (Wilcoxon-test), Q value = 0.042

Table S220.  Gene #58: 'del_15q22.33' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 33(15Q22.33) MUTATED 150 2.4 (3.8)
DEL PEAK 33(15Q22.33) WILD-TYPE 268 1.9 (4.8)

Figure S220.  Get High-res Image Gene #58: 'del_15q22.33' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_16p13.3' versus 'Time to Death'

P value = 0.00603 (logrank test), Q value = 0.041

Table S221.  Gene #59: 'del_16p13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
DEL PEAK 34(16P13.3) MUTATED 52 18 0.2 - 61.8 (19.2)
DEL PEAK 34(16P13.3) WILD-TYPE 378 75 0.0 - 140.4 (20.5)

Figure S221.  Get High-res Image Gene #59: 'del_16p13.3' versus Clinical Feature #1: 'Time to Death'

'del_16p13.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0305 (Fisher's exact test), Q value = 0.13

Table S222.  Gene #59: 'del_16p13.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 34(16P13.3) MUTATED 3 0 3 16 2 0 0 0 9 9 6 5 0
DEL PEAK 34(16P13.3) WILD-TYPE 71 1 25 115 6 1 21 12 47 30 37 13 2

Figure S222.  Get High-res Image Gene #59: 'del_16p13.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_16p13.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0315 (Fisher's exact test), Q value = 0.13

Table S223.  Gene #59: 'del_16p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 11 78 301 52
DEL PEAK 34(16P13.3) MUTATED 0 3 44 7
DEL PEAK 34(16P13.3) WILD-TYPE 11 75 257 45

Figure S223.  Get High-res Image Gene #59: 'del_16p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_16p13.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0736 (Wilcoxon-test), Q value = 0.23

Table S224.  Gene #59: 'del_16p13.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 34(16P13.3) MUTATED 53 3.2 (6.0)
DEL PEAK 34(16P13.3) WILD-TYPE 365 1.9 (4.2)

Figure S224.  Get High-res Image Gene #59: 'del_16p13.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_16q23.1' versus 'Time to Death'

P value = 0.0248 (logrank test), Q value = 0.11

Table S225.  Gene #60: 'del_16q23.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
DEL PEAK 35(16Q23.1) MUTATED 57 16 0.9 - 53.0 (18.2)
DEL PEAK 35(16Q23.1) WILD-TYPE 373 77 0.0 - 140.4 (20.6)

Figure S225.  Get High-res Image Gene #60: 'del_16q23.1' versus Clinical Feature #1: 'Time to Death'

'del_17p12' versus 'YEARS_TO_BIRTH'

P value = 0.0174 (Wilcoxon-test), Q value = 0.083

Table S226.  Gene #61: 'del_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 36(17P12) MUTATED 248 65.8 (12.5)
DEL PEAK 36(17P12) WILD-TYPE 193 68.5 (13.5)

Figure S226.  Get High-res Image Gene #61: 'del_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17p12' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00092

Table S227.  Gene #61: 'del_17p12' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 36(17P12) MUTATED 36 0 13 55 1 1 12 11 35 30 33 13 2
DEL PEAK 36(17P12) WILD-TYPE 38 1 15 76 7 0 9 1 21 9 10 5 0

Figure S227.  Get High-res Image Gene #61: 'del_17p12' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_17p12' versus 'PATHOLOGY_N_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00052

Table S228.  Gene #61: 'del_17p12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 36(17P12) MUTATED 118 70 59
DEL PEAK 36(17P12) WILD-TYPE 139 34 22

Figure S228.  Get High-res Image Gene #61: 'del_17p12' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_17p12' versus 'PATHOLOGY_M_STAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.0048

Table S229.  Gene #61: 'del_17p12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 36(17P12) MUTATED 169 48
DEL PEAK 36(17P12) WILD-TYPE 153 14

Figure S229.  Get High-res Image Gene #61: 'del_17p12' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_17p12' versus 'HISTOLOGICAL_TYPE'

P value = 5.14e-06 (Fisher's exact test), Q value = 0.00033

Table S230.  Gene #61: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 36(17P12) MUTATED 229 17
DEL PEAK 36(17P12) WILD-TYPE 152 43

Figure S230.  Get High-res Image Gene #61: 'del_17p12' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_17p12' versus 'NUMBER_OF_LYMPH_NODES'

P value = 8.59e-07 (Wilcoxon-test), Q value = 8.4e-05

Table S231.  Gene #61: 'del_17p12' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 36(17P12) MUTATED 234 2.8 (5.4)
DEL PEAK 36(17P12) WILD-TYPE 184 1.2 (2.5)

Figure S231.  Get High-res Image Gene #61: 'del_17p12' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_17q24.3' versus 'Time to Death'

P value = 0.0809 (logrank test), Q value = 0.25

Table S232.  Gene #62: 'del_17q24.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 430 93 0.0 - 140.4 (20.4)
DEL PEAK 37(17Q24.3) MUTATED 68 20 0.2 - 140.4 (20.5)
DEL PEAK 37(17Q24.3) WILD-TYPE 362 73 0.0 - 139.2 (20.4)

Figure S232.  Get High-res Image Gene #62: 'del_17q24.3' versus Clinical Feature #1: 'Time to Death'

'del_17q24.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00642 (Fisher's exact test), Q value = 0.042

Table S233.  Gene #62: 'del_17q24.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 37(17Q24.3) MUTATED 10 0 4 10 0 0 3 3 7 11 10 7 1
DEL PEAK 37(17Q24.3) WILD-TYPE 64 1 24 121 8 1 18 9 49 28 33 11 1

Figure S233.  Get High-res Image Gene #62: 'del_17q24.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_17q24.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00182 (Fisher's exact test), Q value = 0.018

Table S234.  Gene #62: 'del_17q24.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 37(17Q24.3) MUTATED 27 23 19
DEL PEAK 37(17Q24.3) WILD-TYPE 230 81 62

Figure S234.  Get High-res Image Gene #62: 'del_17q24.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_17q24.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.00146 (Fisher's exact test), Q value = 0.015

Table S235.  Gene #62: 'del_17q24.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 37(17Q24.3) MUTATED 39 18
DEL PEAK 37(17Q24.3) WILD-TYPE 283 44

Figure S235.  Get High-res Image Gene #62: 'del_17q24.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_17q24.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 8.66e-05 (Wilcoxon-test), Q value = 0.0022

Table S236.  Gene #62: 'del_17q24.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 37(17Q24.3) MUTATED 65 3.0 (3.9)
DEL PEAK 37(17Q24.3) WILD-TYPE 353 1.9 (4.5)

Figure S236.  Get High-res Image Gene #62: 'del_17q24.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_18p11.31' versus 'YEARS_TO_BIRTH'

P value = 0.0064 (Wilcoxon-test), Q value = 0.042

Table S237.  Gene #63: 'del_18p11.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 38(18P11.31) MUTATED 241 65.6 (12.2)
DEL PEAK 38(18P11.31) WILD-TYPE 200 68.5 (13.7)

Figure S237.  Get High-res Image Gene #63: 'del_18p11.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_18p11.31' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00132 (Fisher's exact test), Q value = 0.014

Table S238.  Gene #63: 'del_18p11.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 38(18P11.31) MUTATED 36 0 10 65 2 1 9 8 33 22 32 16 1
DEL PEAK 38(18P11.31) WILD-TYPE 38 1 18 66 6 0 12 4 23 17 11 2 1

Figure S238.  Get High-res Image Gene #63: 'del_18p11.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_18p11.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.0223 (Fisher's exact test), Q value = 0.1

Table S239.  Gene #63: 'del_18p11.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 38(18P11.31) MUTATED 126 67 47
DEL PEAK 38(18P11.31) WILD-TYPE 131 37 34

Figure S239.  Get High-res Image Gene #63: 'del_18p11.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_18p11.31' versus 'PATHOLOGY_M_STAGE'

P value = 2.22e-05 (Fisher's exact test), Q value = 0.00092

Table S240.  Gene #63: 'del_18p11.31' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 38(18P11.31) MUTATED 161 49
DEL PEAK 38(18P11.31) WILD-TYPE 161 13

Figure S240.  Get High-res Image Gene #63: 'del_18p11.31' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_18p11.31' versus 'HISTOLOGICAL_TYPE'

P value = 1.74e-10 (Fisher's exact test), Q value = 1.4e-07

Table S241.  Gene #63: 'del_18p11.31' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 38(18P11.31) MUTATED 229 10
DEL PEAK 38(18P11.31) WILD-TYPE 152 50

Figure S241.  Get High-res Image Gene #63: 'del_18p11.31' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_18p11.31' versus 'COMPLETENESS_OF_RESECTION'

P value = 0.026 (Fisher's exact test), Q value = 0.11

Table S242.  Gene #63: 'del_18p11.31' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

nPatients R0 R1 R2 RX
ALL 316 3 24 25
DEL PEAK 38(18P11.31) MUTATED 169 0 18 11
DEL PEAK 38(18P11.31) WILD-TYPE 147 3 6 14

Figure S242.  Get High-res Image Gene #63: 'del_18p11.31' versus Clinical Feature #10: 'COMPLETENESS_OF_RESECTION'

'del_18p11.31' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0255 (Wilcoxon-test), Q value = 0.11

Table S243.  Gene #63: 'del_18p11.31' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 38(18P11.31) MUTATED 227 2.2 (4.1)
DEL PEAK 38(18P11.31) WILD-TYPE 191 1.9 (4.9)

Figure S243.  Get High-res Image Gene #63: 'del_18p11.31' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_18q12.2' versus 'YEARS_TO_BIRTH'

P value = 0.0177 (Wilcoxon-test), Q value = 0.084

Table S244.  Gene #64: 'del_18q12.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 39(18Q12.2) MUTATED 268 66.0 (12.3)
DEL PEAK 39(18Q12.2) WILD-TYPE 173 68.5 (13.9)

Figure S244.  Get High-res Image Gene #64: 'del_18q12.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_18q12.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00056 (Fisher's exact test), Q value = 0.008

Table S245.  Gene #64: 'del_18q12.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 39(18Q12.2) MUTATED 38 0 15 69 2 1 11 11 37 27 35 14 1
DEL PEAK 39(18Q12.2) WILD-TYPE 36 1 13 62 6 0 10 1 19 12 8 4 1

Figure S245.  Get High-res Image Gene #64: 'del_18q12.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_18q12.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00087 (Fisher's exact test), Q value = 0.011

Table S246.  Gene #64: 'del_18q12.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 39(18Q12.2) MUTATED 136 73 58
DEL PEAK 39(18Q12.2) WILD-TYPE 121 31 23

Figure S246.  Get High-res Image Gene #64: 'del_18q12.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_18q12.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.000911 (Fisher's exact test), Q value = 0.011

Table S247.  Gene #64: 'del_18q12.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 39(18Q12.2) MUTATED 187 50
DEL PEAK 39(18Q12.2) WILD-TYPE 135 12

Figure S247.  Get High-res Image Gene #64: 'del_18q12.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_18q12.2' versus 'HISTOLOGICAL_TYPE'

P value = 3.04e-09 (Fisher's exact test), Q value = 1.1e-06

Table S248.  Gene #64: 'del_18q12.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 39(18Q12.2) MUTATED 252 15
DEL PEAK 39(18Q12.2) WILD-TYPE 129 45

Figure S248.  Get High-res Image Gene #64: 'del_18q12.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_18q12.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00158 (Wilcoxon-test), Q value = 0.016

Table S249.  Gene #64: 'del_18q12.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 39(18Q12.2) MUTATED 254 2.3 (4.6)
DEL PEAK 39(18Q12.2) WILD-TYPE 164 1.7 (4.1)

Figure S249.  Get High-res Image Gene #64: 'del_18q12.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_18q21.2' versus 'YEARS_TO_BIRTH'

P value = 0.0349 (Wilcoxon-test), Q value = 0.13

Table S250.  Gene #65: 'del_18q21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 441 67.0 (13.0)
DEL PEAK 40(18Q21.2) MUTATED 282 66.1 (12.3)
DEL PEAK 40(18Q21.2) WILD-TYPE 159 68.4 (14.1)

Figure S250.  Get High-res Image Gene #65: 'del_18q21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_18q21.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0018

Table S251.  Gene #65: 'del_18q21.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 40(18Q21.2) MUTATED 40 0 16 71 2 1 11 11 40 30 37 15 2
DEL PEAK 40(18Q21.2) WILD-TYPE 34 1 12 60 6 0 10 1 16 9 6 3 0

Figure S251.  Get High-res Image Gene #65: 'del_18q21.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_18q21.2' versus 'PATHOLOGY_N_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.0014

Table S252.  Gene #65: 'del_18q21.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 40(18Q21.2) MUTATED 141 77 63
DEL PEAK 40(18Q21.2) WILD-TYPE 116 27 18

Figure S252.  Get High-res Image Gene #65: 'del_18q21.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_18q21.2' versus 'PATHOLOGY_M_STAGE'

P value = 3.53e-05 (Fisher's exact test), Q value = 0.0013

Table S253.  Gene #65: 'del_18q21.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 40(18Q21.2) MUTATED 195 54
DEL PEAK 40(18Q21.2) WILD-TYPE 127 8

Figure S253.  Get High-res Image Gene #65: 'del_18q21.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_18q21.2' versus 'GENDER'

P value = 0.0606 (Fisher's exact test), Q value = 0.2

Table S254.  Gene #65: 'del_18q21.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 210 233
DEL PEAK 40(18Q21.2) MUTATED 124 158
DEL PEAK 40(18Q21.2) WILD-TYPE 86 75

Figure S254.  Get High-res Image Gene #65: 'del_18q21.2' versus Clinical Feature #7: 'GENDER'

'del_18q21.2' versus 'HISTOLOGICAL_TYPE'

P value = 3.88e-09 (Fisher's exact test), Q value = 1.1e-06

Table S255.  Gene #65: 'del_18q21.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 40(18Q21.2) MUTATED 264 17
DEL PEAK 40(18Q21.2) WILD-TYPE 117 43

Figure S255.  Get High-res Image Gene #65: 'del_18q21.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_18q21.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 4.33e-05 (Wilcoxon-test), Q value = 0.0014

Table S256.  Gene #65: 'del_18q21.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 40(18Q21.2) MUTATED 268 2.4 (4.6)
DEL PEAK 40(18Q21.2) WILD-TYPE 150 1.5 (4.1)

Figure S256.  Get High-res Image Gene #65: 'del_18q21.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_19p13.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00723 (Fisher's exact test), Q value = 0.045

Table S257.  Gene #66: 'del_19p13.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 41(19P13.3) MUTATED 8 0 1 11 0 0 4 3 6 12 10 4 1
DEL PEAK 41(19P13.3) WILD-TYPE 66 1 27 120 8 1 17 9 50 27 33 14 1

Figure S257.  Get High-res Image Gene #66: 'del_19p13.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_19p13.3' versus 'PATHOLOGY_N_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.0014

Table S258.  Gene #66: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 41(19P13.3) MUTATED 22 16 24
DEL PEAK 41(19P13.3) WILD-TYPE 235 88 57

Figure S258.  Get High-res Image Gene #66: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_19p13.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0149 (Fisher's exact test), Q value = 0.075

Table S259.  Gene #66: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 41(19P13.3) MUTATED 38 15
DEL PEAK 41(19P13.3) WILD-TYPE 284 47

Figure S259.  Get High-res Image Gene #66: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_19p13.3' versus 'NUMBER_OF_LYMPH_NODES'

P value = 2.68e-06 (Wilcoxon-test), Q value = 2e-04

Table S260.  Gene #66: 'del_19p13.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 41(19P13.3) MUTATED 59 4.3 (6.0)
DEL PEAK 41(19P13.3) WILD-TYPE 359 1.7 (4.1)

Figure S260.  Get High-res Image Gene #66: 'del_19p13.3' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_20p12.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0744 (Fisher's exact test), Q value = 0.23

Table S261.  Gene #67: 'del_20p12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 42(20P12.1) MUTATED 77 6
DEL PEAK 42(20P12.1) WILD-TYPE 304 54

Figure S261.  Get High-res Image Gene #67: 'del_20p12.1' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_21q11.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0272 (Fisher's exact test), Q value = 0.12

Table S262.  Gene #68: 'del_21q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 43(21Q11.2) MUTATED 70 32 35
DEL PEAK 43(21Q11.2) WILD-TYPE 187 72 46

Figure S262.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_21q11.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00141 (Fisher's exact test), Q value = 0.015

Table S263.  Gene #68: 'del_21q11.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 43(21Q11.2) MUTATED 127 8
DEL PEAK 43(21Q11.2) WILD-TYPE 254 52

Figure S263.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_21q11.2' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0309 (Wilcoxon-test), Q value = 0.13

Table S264.  Gene #68: 'del_21q11.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 43(21Q11.2) MUTATED 130 3.0 (6.3)
DEL PEAK 43(21Q11.2) WILD-TYPE 288 1.7 (3.2)

Figure S264.  Get High-res Image Gene #68: 'del_21q11.2' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'del_22q13.32' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00562 (Fisher's exact test), Q value = 0.04

Table S265.  Gene #69: 'del_22q13.32' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 28 131 8 1 21 12 56 39 43 18 2
DEL PEAK 44(22Q13.32) MUTATED 19 0 7 39 1 0 7 7 19 21 24 8 0
DEL PEAK 44(22Q13.32) WILD-TYPE 55 1 21 92 7 1 14 5 37 18 19 10 2

Figure S265.  Get High-res Image Gene #69: 'del_22q13.32' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_22q13.32' versus 'PATHOLOGY_N_STAGE'

P value = 0.00018 (Fisher's exact test), Q value = 0.0038

Table S266.  Gene #69: 'del_22q13.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 257 104 81
DEL PEAK 44(22Q13.32) MUTATED 71 45 40
DEL PEAK 44(22Q13.32) WILD-TYPE 186 59 41

Figure S266.  Get High-res Image Gene #69: 'del_22q13.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_22q13.32' versus 'PATHOLOGY_M_STAGE'

P value = 0.00372 (Fisher's exact test), Q value = 0.03

Table S267.  Gene #69: 'del_22q13.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 322 62
DEL PEAK 44(22Q13.32) MUTATED 103 32
DEL PEAK 44(22Q13.32) WILD-TYPE 219 30

Figure S267.  Get High-res Image Gene #69: 'del_22q13.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_22q13.32' versus 'HISTOLOGICAL_TYPE'

P value = 0.00337 (Fisher's exact test), Q value = 0.028

Table S268.  Gene #69: 'del_22q13.32' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 381 60
DEL PEAK 44(22Q13.32) MUTATED 145 11
DEL PEAK 44(22Q13.32) WILD-TYPE 236 49

Figure S268.  Get High-res Image Gene #69: 'del_22q13.32' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'del_22q13.32' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000117 (Wilcoxon-test), Q value = 0.0027

Table S269.  Gene #69: 'del_22q13.32' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 418 2.1 (4.5)
DEL PEAK 44(22Q13.32) MUTATED 147 2.9 (4.9)
DEL PEAK 44(22Q13.32) WILD-TYPE 271 1.7 (4.2)

Figure S269.  Get High-res Image Gene #69: 'del_22q13.32' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/15082914/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/COAD-TP/15076851/COAD-TP.merged_data.txt

  • Number of patients = 443

  • Number of significantly focal cnvs = 69

  • Number of selected clinical features = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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