Correlation between copy number variations of arm-level result and selected clinical features
Colon Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1GF0SW2
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1GF0SW2
Overview
Introduction

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

Summary

Testing the association between copy number variation 81 arm-level events and 13 clinical features across 449 patients, 174 significant findings detected with Q value < 0.25.

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

  • 3p gain cnv correlated to 'PATHOLOGIC_STAGE'.

  • 3q gain cnv correlated to 'PATHOLOGIC_STAGE'.

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

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

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

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

  • 6q gain cnv correlated to 'PATHOLOGY_N_STAGE'.

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

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

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

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

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

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

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

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

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

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

  • 14q gain cnv correlated to 'RACE'.

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

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

  • 17q gain cnv correlated to 'ETHNICITY'.

  • 18p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 18q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

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

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

  • 21q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • xp gain cnv correlated to 'PATHOLOGY_T_STAGE'.

  • xq gain cnv correlated to 'PATHOLOGY_T_STAGE'.

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

  • 3p loss cnv correlated to 'PATHOLOGY_M_STAGE'.

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

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

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

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

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

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

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

  • 9p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 9q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 10p loss cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_M_STAGE'.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 81 arm-level events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 174 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		RESIDUAL
TUMOR 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test
11p gain 54 (12%) 395 0.461
(0.853) 		0.0133
(0.132) 		0.0245
(0.18) 		0.0557
(0.305) 		0.0159
(0.142) 		0.00868
(0.106) 		0.885
(1.00) 		1
(1.00) 		0.0194
(0.156) 		0.329
(0.751) 		0.0147
(0.139) 		0.6
(0.932) 		0.434
(0.831)
13q gain 255 (57%) 194 0.545
(0.913) 		0.615
(0.933) 		0.00152
(0.0369) 		0.984
(1.00) 		0.00495
(0.0789) 		0.00555
(0.0789) 		0.504
(0.879) 		0.745
(1.00) 		6.79e-07
(0.000119) 		0.0329
(0.222) 		0.00961
(0.112) 		0.242
(0.673) 		0.639
(0.944)
17p loss 234 (52%) 215 0.15
(0.531) 		0.0995
(0.424) 		6e-05
(0.00632) 		0.658
(0.947) 		0.0003
(0.0155) 		0.000329
(0.0155) 		0.0381
(0.238) 		1
(1.00) 		5.27e-07
(0.000111) 		0.074
(0.366) 		7.47e-05
(0.00715) 		0.868
(1.00) 		1
(1.00)
18p loss 251 (56%) 198 0.859
(1.00) 		0.023
(0.173) 		0.00095
(0.0294) 		0.926
(1.00) 		0.0121
(0.129) 		2.92e-05
(0.00385) 		0.343
(0.762) 		1
(1.00) 		8e-11
(8.43e-08) 		0.124
(0.49) 		0.00527
(0.0789) 		0.881
(1.00) 		0.635
(0.94)
18q loss 267 (59%) 182 0.959
(1.00) 		0.0118
(0.127) 		0.00048
(0.0202) 		0.828
(1.00) 		0.00127
(0.0334) 		0.000145
(0.0109) 		0.291
(0.716) 		0.743
(1.00) 		3.46e-10
(1.82e-07) 		0.225
(0.647) 		0.00108
(0.0316) 		0.933
(1.00) 		1
(1.00)
7p gain 245 (55%) 204 0.954
(1.00) 		0.142
(0.521) 		5e-05
(0.00585) 		0.272
(0.703) 		0.00011
(0.00965) 		0.0197
(0.156) 		0.85
(1.00) 		0.522
(0.892) 		0.0189
(0.156) 		0.324
(0.751) 		0.000584
(0.0212) 		0.721
(0.988) 		1
(1.00)
7q gain 222 (49%) 227 0.811
(1.00) 		0.0818
(0.386) 		0.0109
(0.122) 		0.141
(0.52) 		0.0123
(0.13) 		0.0139
(0.134) 		1
(1.00) 		0.747
(1.00) 		0.0406
(0.247) 		0.402
(0.807) 		0.0128
(0.131) 		0.484
(0.86) 		1
(1.00)
11q gain 51 (11%) 398 0.712
(0.983) 		0.000379
(0.0166) 		0.0187
(0.156) 		0.228
(0.648) 		0.0114
(0.125) 		0.0775
(0.372) 		1
(1.00) 		1
(1.00) 		0.00467
(0.0759) 		0.47
(0.86) 		0.0131
(0.132) 		0.711
(0.983) 		0.405
(0.807)
20q gain 319 (71%) 130 0.9
(1.00) 		0.264
(0.699) 		0.013
(0.131) 		0.215
(0.629) 		0.0168
(0.145) 		0.00404
(0.0709) 		0.211
(0.629) 		1
(1.00) 		2.72e-07
(8.95e-05) 		0.16
(0.557) 		0.0255
(0.185) 		0.69
(0.97) 		1
(1.00)
1p loss 92 (20%) 357 0.00763
(0.0956) 		0.921
(1.00) 		0.00894
(0.108) 		0.44
(0.837) 		0.00188
(0.0412) 		0.00205
(0.0441) 		0.294
(0.716) 		0.214
(0.629) 		0.238
(0.663) 		0.361
(0.778) 		0.000702
(0.0238) 		0.384
(0.795) 		0.193
(0.611)
4p loss 137 (31%) 312 0.0997
(0.424) 		0.928
(1.00) 		0.00256
(0.0518) 		0.332
(0.751) 		0.00466
(0.0759) 		2.45e-05
(0.00368) 		0.918
(1.00) 		0.467
(0.859) 		0.00726
(0.0946) 		0.0728
(0.362) 		0.00154
(0.0369) 		0.636
(0.94) 		0.077
(0.372)
8p loss 136 (30%) 313 0.564
(0.919) 		0.754
(1.00) 		0.00749
(0.095) 		0.262
(0.695) 		0.00052
(0.0208) 		0.000571
(0.0212) 		0.125
(0.49) 		0.726
(0.99) 		0.0247
(0.18) 		0.0865
(0.4) 		0.000222
(0.0133) 		0.251
(0.682) 		0.0969
(0.42)
22q loss 144 (32%) 305 0.11
(0.452) 		0.724
(0.99) 		0.00019
(0.0125) 		0.554
(0.919) 		0.00014
(0.0109) 		0.00122
(0.0328) 		0.84
(1.00) 		1
(1.00) 		0.00316
(0.0617) 		0.397
(0.807) 		0.000273
(0.0151) 		0.315
(0.745) 		0.591
(0.932)
4q gain 17 (4%) 432 0.172
(0.574) 		0.992
(1.00) 		0.226
(0.648) 		0.603
(0.932) 		0.00252
(0.0518) 		0.0155
(0.141) 		0.63
(0.939) 		1
(1.00) 		0.488
(0.862) 		0.419
(0.817) 		0.00165
(0.0386) 		0.0325
(0.222) 		1
(1.00)
9p gain 81 (18%) 368 0.00621
(0.086) 		0.339
(0.755) 		0.0194
(0.156) 		0.471
(0.86) 		0.275
(0.703) 		0.14
(0.52) 		0.714
(0.983) 		0.655
(0.946) 		0.0218
(0.167) 		0.903
(1.00) 		0.246
(0.676) 		0.0163
(0.143) 		0.154
(0.543)
16p gain 106 (24%) 343 0.314
(0.745) 		0.175
(0.576) 		0.0046
(0.0759) 		0.907
(1.00) 		0.00687
(0.0916) 		0.329
(0.751) 		1
(1.00) 		1
(1.00) 		0.00116
(0.0321) 		0.984
(1.00) 		0.00542
(0.0789) 		0.366
(0.781) 		1
(1.00)
16q gain 104 (23%) 345 0.296
(0.718) 		0.129
(0.495) 		0.00104
(0.0313) 		0.919
(1.00) 		0.00363
(0.0683) 		0.624
(0.935) 		0.911
(1.00) 		1
(1.00) 		0.00177
(0.0406) 		0.847
(1.00) 		0.00524
(0.0789) 		0.402
(0.807) 		1
(1.00)
4q loss 125 (28%) 324 0.0661
(0.339) 		0.955
(1.00) 		0.0203
(0.157) 		0.481
(0.86) 		0.00521
(0.0789) 		0.0135
(0.132) 		0.916
(1.00) 		0.286
(0.716) 		0.0663
(0.339) 		0.321
(0.75) 		0.00225
(0.0474) 		0.304
(0.727) 		0.0644
(0.336)
5q loss 80 (18%) 369 0.047
(0.269) 		0.252
(0.682) 		0.0362
(0.232) 		0.886
(1.00) 		0.00377
(0.0685) 		0.044
(0.258) 		0.266
(0.699) 		1
(1.00) 		0.157
(0.547) 		0.361
(0.778) 		0.00113
(0.0321) 		0.32
(0.75) 		0.0228
(0.173)
15q loss 157 (35%) 292 0.331
(0.751) 		0.625
(0.935) 		0.0516
(0.291) 		0.611
(0.932) 		0.0382
(0.238) 		0.000946
(0.0294) 		0.692
(0.97) 		0.727
(0.991) 		0.0145
(0.139) 		0.675
(0.959) 		0.0199
(0.157) 		0.342
(0.761) 		0.617
(0.935)
19p loss 40 (9%) 409 0.144
(0.523) 		0.151
(0.532) 		0.00551
(0.0789) 		1
(1.00) 		0.00142
(0.0356) 		0.00553
(0.0789) 		0.743
(1.00) 		0.564
(0.919) 		0.467
(0.859) 		0.324
(0.751) 		0.000156
(0.0109) 		0.758
(1.00) 		1
(1.00)
19q loss 33 (7%) 416 0.206
(0.622) 		0.477
(0.86) 		0.0161
(0.142) 		0.934
(1.00) 		0.00064
(0.0225) 		0.0302
(0.211) 		0.718
(0.986) 		0.476
(0.86) 		0.426
(0.822) 		0.404
(0.807) 		0.000533
(0.0208) 		0.104
(0.436) 		1
(1.00)
4p gain 12 (3%) 437 0.91
(1.00) 		0.26
(0.693) 		0.212
(0.629) 		0.649
(0.946) 		0.0263
(0.19) 		0.168
(0.569) 		0.389
(0.8) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0152
(0.141) 		0.00361
(0.0683) 		1
(1.00)
12q gain 88 (20%) 361 0.962
(1.00) 		0.103
(0.433) 		0.0168
(0.145) 		0.425
(0.822) 		0.0368
(0.235) 		0.3
(0.725) 		0.812
(1.00) 		0.674
(0.959) 		0.122
(0.486) 		0.423
(0.821) 		0.0149
(0.14) 		0.823
(1.00) 		1
(1.00)
20p gain 242 (54%) 207 0.275
(0.703) 		0.484
(0.86) 		0.00384
(0.0685) 		0.747
(1.00) 		0.101
(0.429) 		0.000936
(0.0294) 		0.218
(0.636) 		0.516
(0.889) 		0.000323
(0.0155) 		0.126
(0.49) 		0.0651
(0.338) 		0.971
(1.00) 		0.35
(0.766)
6q loss 45 (10%) 404 0.0188
(0.156) 		0.797
(1.00) 		0.749
(1.00) 		0.283
(0.714) 		0.0484
(0.275) 		0.166
(0.567) 		0.53
(0.9) 		0.207
(0.622) 		0.65
(0.946) 		0.177
(0.576) 		0.00669
(0.0903) 		0.0129
(0.131) 		1
(1.00)
12q loss 50 (11%) 399 0.291
(0.716) 		0.336
(0.752) 		0.0588
(0.314) 		0.615
(0.933) 		0.0349
(0.228) 		0.177
(0.576) 		0.549
(0.916) 		0.607
(0.932) 		0.0294
(0.207) 		1
(1.00) 		0.0115
(0.125) 		0.458
(0.853) 		1
(1.00)
17q loss 64 (14%) 385 0.0918
(0.413) 		0.965
(1.00) 		0.052
(0.291) 		0.46
(0.853) 		0.00651
(0.089) 		0.0235
(0.176) 		1
(1.00) 		0.627
(0.935) 		0.847
(1.00) 		0.535
(0.906) 		0.000339
(0.0155) 		0.161
(0.557) 		1
(1.00)
21q loss 123 (27%) 326 0.875
(1.00) 		0.961
(1.00) 		0.449
(0.846) 		0.475
(0.86) 		0.032
(0.22) 		0.124
(0.49) 		0.916
(1.00) 		0.714
(0.983) 		0.00542
(0.0789) 		0.591
(0.932) 		0.0387
(0.239) 		0.432
(0.828) 		0.0668
(0.34)
xp loss 63 (14%) 386 0.0965
(0.42) 		0.798
(1.00) 		0.172
(0.574) 		0.204
(0.622) 		0.00138
(0.0354) 		0.0334
(0.223) 		0.134
(0.508) 		0.619
(0.935) 		0.33
(0.751) 		0.739
(1.00) 		0.000228
(0.0133) 		0.562
(0.919) 		1
(1.00)
xq loss 50 (11%) 399 0.402
(0.807) 		0.899
(1.00) 		0.203
(0.622) 		0.115
(0.464) 		0.024
(0.178) 		0.00997
(0.114) 		0.295
(0.717) 		0.606
(0.932) 		0.829
(1.00) 		0.35
(0.766) 		0.00851
(0.105) 		0.476
(0.86) 		1
(1.00)
1q gain 81 (18%) 368 0.305
(0.727) 		0.771
(1.00) 		0.362
(0.778) 		0.518
(0.89) 		0.0921
(0.413) 		0.00727
(0.0946) 		0.085
(0.398) 		0.67
(0.959) 		0.156
(0.547) 		0.281
(0.711) 		0.0201
(0.157) 		1
(1.00) 		1
(1.00)
5p gain 68 (15%) 381 0.776
(1.00) 		0.0756
(0.368) 		0.0913
(0.413) 		0.953
(1.00) 		0.0154
(0.141) 		0.174
(0.576) 		0.236
(0.662) 		1
(1.00) 		0.705
(0.98) 		0.354
(0.77) 		0.0095
(0.112) 		0.229
(0.65) 		1
(1.00)
6p gain 84 (19%) 365 0.833
(1.00) 		0.816
(1.00) 		0.198
(0.621) 		0.935
(1.00) 		0.0304
(0.211) 		0.484
(0.86) 		0.397
(0.807) 		0.674
(0.959) 		0.482
(0.86) 		0.647
(0.946) 		0.0352
(0.229) 		0.301
(0.725) 		1
(1.00)
8q gain 226 (50%) 223 0.712
(0.983) 		0.0343
(0.226) 		0.349
(0.766) 		0.293
(0.716) 		0.377
(0.79) 		0.0777
(0.372) 		0.571
(0.923) 		0.751
(1.00) 		0.0134
(0.132) 		0.201
(0.622) 		0.324
(0.751) 		0.798
(1.00) 		0.625
(0.935)
9q gain 71 (16%) 378 0.00994
(0.114) 		0.407
(0.807) 		0.232
(0.655) 		0.501
(0.877) 		0.518
(0.89) 		0.25
(0.681) 		1
(1.00) 		0.627
(0.935) 		0.0378
(0.238) 		0.976
(1.00) 		0.365
(0.781) 		0.18
(0.582) 		0.48
(0.86)
10q gain 23 (5%) 426 0.626
(0.935) 		0.0825
(0.388) 		0.493
(0.87) 		0.911
(1.00) 		0.227
(0.648) 		0.497
(0.874) 		0.522
(0.892) 		0.358
(0.773) 		0.546
(0.913) 		0.735
(0.998) 		0.0794
(0.378) 		0.0197
(0.156) 		0.0181
(0.154)
5p loss 60 (13%) 389 0.247
(0.679) 		0.643
(0.946) 		0.0151
(0.141) 		0.726
(0.99) 		0.118
(0.474) 		0.316
(0.745) 		0.781
(1.00) 		1
(1.00) 		0.23
(0.65) 		0.0998
(0.424) 		0.113
(0.459) 		0.416
(0.817) 		0.0106
(0.12)
6p loss 33 (7%) 416 0.0384
(0.238) 		0.19
(0.608) 		0.714
(0.983) 		0.143
(0.523) 		0.938
(1.00) 		0.43
(0.826) 		0.37
(0.782) 		0.146
(0.527) 		0.791
(1.00) 		0.112
(0.456) 		0.936
(1.00) 		0.0294
(0.207) 		1
(1.00)
10p loss 67 (15%) 382 0.84
(1.00) 		0.128
(0.495) 		0.0397
(0.243) 		0.952
(1.00) 		0.141
(0.52) 		0.0195
(0.156) 		0.791
(1.00) 		0.181
(0.586) 		0.252
(0.682) 		0.506
(0.881) 		0.0594
(0.316) 		0.576
(0.927) 		0.524
(0.894)
11p loss 50 (11%) 399 0.647
(0.946) 		0.483
(0.86) 		0.436
(0.832) 		0.874
(1.00) 		0.0371
(0.235) 		0.0775
(0.372) 		0.881
(1.00) 		1
(1.00) 		1
(1.00) 		0.504
(0.879) 		0.00906
(0.108) 		0.418
(0.817) 		1
(1.00)
11q loss 62 (14%) 387 0.417
(0.817) 		0.415
(0.817) 		0.265
(0.699) 		0.284
(0.714) 		0.0529
(0.295) 		0.0161
(0.142) 		0.496
(0.874) 		1
(1.00) 		1
(1.00) 		0.438
(0.834) 		0.0411
(0.249) 		0.406
(0.807) 		1
(1.00)
12p loss 48 (11%) 401 0.168
(0.569) 		0.236
(0.662) 		0.227
(0.648) 		0.563
(0.919) 		0.0747
(0.366) 		0.253
(0.682) 		0.761
(1.00) 		1
(1.00) 		0.00741
(0.095) 		0.961
(1.00) 		0.0327
(0.222) 		0.89
(1.00) 		1
(1.00)
13q loss 12 (3%) 437 0.452
(0.848) 		0.995
(1.00) 		0.805
(1.00) 		0.452
(0.848) 		0.099
(0.424) 		0.622
(0.935) 		0.775
(1.00) 		1
(1.00) 		0.188
(0.605) 		0.823
(1.00) 		0.0129
(0.131) 		0.0191
(0.156) 		1
(1.00)
14q loss 137 (31%) 312 0.811
(1.00) 		0.392
(0.804) 		0.176
(0.576) 		0.345
(0.763) 		0.135
(0.508) 		0.0116
(0.125) 		0.918
(1.00) 		0.724
(0.99) 		3.4e-07
(8.95e-05) 		0.584
(0.93) 		0.208
(0.622) 		0.872
(1.00) 		1
(1.00)
3p gain 47 (10%) 402 0.289
(0.716) 		0.0899
(0.41) 		0.003
(0.0596) 		0.943
(1.00) 		0.328
(0.751) 		0.335
(0.752) 		0.645
(0.946) 		0.606
(0.932) 		0.656
(0.946) 		0.53
(0.9) 		0.208
(0.622) 		0.204
(0.622) 		1
(1.00)
3q gain 64 (14%) 385 0.0567
(0.308) 		0.39
(0.8) 		0.00562
(0.0789) 		0.606
(0.932) 		0.095
(0.417) 		0.0633
(0.333) 		0.687
(0.968) 		0.367
(0.781) 		0.33
(0.751) 		0.655
(0.946) 		0.166
(0.567) 		0.257
(0.687) 		0.48
(0.86)
6q gain 76 (17%) 373 0.528
(0.9) 		0.571
(0.923) 		0.086
(0.399) 		0.983
(1.00) 		0.0354
(0.229) 		0.272
(0.703) 		0.802
(1.00) 		0.648
(0.946) 		0.466
(0.859) 		0.867
(1.00) 		0.056
(0.305) 		0.862
(1.00) 		1
(1.00)
14q gain 35 (8%) 414 0.584
(0.93) 		0.788
(1.00) 		0.446
(0.843) 		0.859
(1.00) 		0.475
(0.86) 		0.302
(0.725) 		0.601
(0.932) 		1
(1.00) 		0.0699
(0.352) 		0.279
(0.707) 		0.289
(0.716) 		0.0229
(0.173) 		1
(1.00)
17q gain 84 (19%) 365 0.131
(0.502) 		0.355
(0.771) 		0.149
(0.531) 		0.268
(0.701) 		0.198
(0.622) 		0.0744
(0.366) 		0.904
(1.00) 		0.686
(0.968) 		0.291
(0.716) 		0.386
(0.796) 		0.917
(1.00) 		0.798
(1.00) 		0.0282
(0.202)
18p gain 23 (5%) 426 0.335
(0.752) 		0.417
(0.817) 		0.0727
(0.362) 		1
(1.00) 		0.0448
(0.26) 		1
(1.00) 		0.284
(0.714) 		1
(1.00) 		0.0291
(0.207) 		0.566
(0.921) 		0.0455
(0.262) 		0.55
(0.917) 		1
(1.00)
18q gain 14 (3%) 435 0.62
(0.935) 		0.0635
(0.333) 		0.266
(0.699) 		0.83
(1.00) 		0.483
(0.86) 		0.699
(0.978) 		0.425
(0.822) 		1
(1.00) 		0.0331
(0.222) 		1
(1.00) 		0.777
(1.00) 		0.221
(0.64) 		1
(1.00)
21q gain 24 (5%) 425 0.818
(1.00) 		0.00186
(0.0412) 		0.333
(0.752) 		0.105
(0.439) 		0.293
(0.716) 		0.512
(0.886) 		0.534
(0.906) 		0.358
(0.773) 		0.347
(0.765) 		0.451
(0.848) 		0.135
(0.508) 		0.606
(0.932) 		1
(1.00)
xp gain 68 (15%) 381 0.733
(0.998) 		0.741
(1.00) 		0.249
(0.681) 		0.0179
(0.154) 		0.442
(0.838) 		0.846
(1.00) 		0.148
(0.53) 		0.622
(0.935) 		1
(1.00) 		0.921
(1.00) 		0.922
(1.00) 		0.649
(0.946) 		1
(1.00)
xq gain 79 (18%) 370 0.643
(0.946) 		0.51
(0.884) 		0.0441
(0.258) 		0.00384
(0.0685) 		0.556
(0.919) 		0.857
(1.00) 		0.267
(0.7) 		0.655
(0.946) 		0.592
(0.932) 		0.919
(1.00) 		0.487
(0.862) 		0.542
(0.911) 		1
(1.00)
3p loss 53 (12%) 396 0.176
(0.576) 		0.672
(0.959) 		0.419
(0.817) 		0.148
(0.53) 		0.108
(0.448) 		0.0343
(0.226) 		1
(1.00) 		0.609
(0.932) 		0.204
(0.622) 		0.901
(1.00) 		0.0935
(0.414) 		0.564
(0.919) 		0.405
(0.807)
9p loss 53 (12%) 396 0.752
(1.00) 		0.394
(0.805) 		0.859
(1.00) 		0.175
(0.576) 		0.367
(0.781) 		0.404
(0.807) 		0.145
(0.526) 		0.612
(0.932) 		0.00469
(0.0759) 		0.172
(0.574) 		0.123
(0.49) 		0.804
(1.00) 		0.424
(0.822)
9q loss 53 (12%) 396 0.674
(0.959) 		0.0944
(0.416) 		0.7
(0.978) 		0.114
(0.463) 		0.275
(0.703) 		0.0861
(0.399) 		0.561
(0.919) 		0.612
(0.932) 		0.00467
(0.0759) 		0.661
(0.95) 		0.169
(0.569) 		0.857
(1.00) 		0.443
(0.84)
1p gain 40 (9%) 409 0.954
(1.00) 		0.57
(0.923) 		0.97
(1.00) 		0.597
(0.932) 		0.829
(1.00) 		0.217
(0.636) 		0.407
(0.807) 		0.564
(0.919) 		0.336
(0.752) 		0.243
(0.673) 		0.412
(0.815) 		0.653
(0.946) 		0.384
(0.795)
2p gain 82 (18%) 367 0.455
(0.85) 		0.995
(1.00) 		0.539
(0.911) 		0.46
(0.853) 		0.169
(0.569) 		0.469
(0.86) 		0.714
(0.983) 		0.678
(0.961) 		0.157
(0.547) 		0.131
(0.502) 		0.12
(0.481) 		0.671
(0.959) 		0.199
(0.622)
2q gain 79 (18%) 370 0.379
(0.791) 		0.541
(0.911) 		0.262
(0.695) 		0.373
(0.782) 		0.0436
(0.258) 		0.58
(0.93) 		0.804
(1.00) 		0.666
(0.956) 		0.209
(0.622) 		0.209
(0.622) 		0.0421
(0.253) 		0.508
(0.883) 		0.182
(0.586)
5q gain 40 (9%) 409 0.544
(0.913) 		0.825
(1.00) 		0.195
(0.615) 		0.911
(1.00) 		0.213
(0.629) 		0.459
(0.853) 		0.512
(0.886) 		0.575
(0.927) 		0.632
(0.939) 		0.335
(0.752) 		0.746
(1.00) 		0.373
(0.782) 		1
(1.00)
8p gain 134 (30%) 315 0.94
(1.00) 		0.14
(0.52) 		0.868
(1.00) 		0.763
(1.00) 		0.429
(0.826) 		0.764
(1.00) 		0.836
(1.00) 		0.29
(0.716) 		0.37
(0.782) 		0.269
(0.701) 		0.484
(0.86) 		0.918
(1.00) 		1
(1.00)
10p gain 38 (8%) 411 0.0437
(0.258) 		0.603
(0.932) 		0.318
(0.749) 		0.345
(0.763) 		0.0437
(0.258) 		0.316
(0.745) 		0.738
(1.00) 		1
(1.00) 		0.632
(0.939) 		0.611
(0.932) 		0.071
(0.356) 		0.112
(0.456) 		0.0535
(0.297)
12p gain 93 (21%) 356 0.402
(0.807) 		0.291
(0.716) 		0.133
(0.507) 		0.372
(0.782) 		0.203
(0.622) 		0.866
(1.00) 		0.907
(1.00) 		0.682
(0.965) 		0.315
(0.745) 		0.582
(0.93) 		0.103
(0.433) 		1
(1.00) 		1
(1.00)
15q gain 11 (2%) 438 0.857
(1.00) 		0.483
(0.86) 		0.586
(0.932) 		0.42
(0.817) 		0.915
(1.00) 		0.0869
(0.4) 		0.126
(0.49) 		1
(1.00) 		1
(1.00) 		0.407
(0.807) 		0.553
(0.919) 		0.346
(0.764) 		1
(1.00)
17p gain 29 (6%) 420 0.0672
(0.34) 		0.618
(0.935) 		0.583
(0.93) 		0.867
(1.00) 		0.327
(0.751) 		0.558
(0.919) 		0.702
(0.979) 		1
(1.00) 		0.58
(0.93) 		0.919
(1.00) 		0.703
(0.979) 		0.0552
(0.305) 		0.275
(0.703)
19p gain 73 (16%) 376 0.297
(0.719) 		0.973
(1.00) 		0.747
(1.00) 		0.691
(0.97) 		0.171
(0.574) 		0.56
(0.919) 		0.097
(0.42) 		0.175
(0.576) 		0.579
(0.93) 		0.106
(0.441) 		0.867
(1.00) 		1
(1.00) 		1
(1.00)
19q gain 84 (19%) 365 0.461
(0.853) 		0.972
(1.00) 		0.768
(1.00) 		0.791
(1.00) 		0.192
(0.61) 		0.272
(0.703) 		0.276
(0.703) 		0.383
(0.795) 		1
(1.00) 		0.244
(0.675) 		0.917
(1.00) 		0.914
(1.00) 		1
(1.00)
22q gain 12 (3%) 437 0.716
(0.985) 		0.548
(0.916) 		0.646
(0.946) 		0.256
(0.687) 		1
(1.00) 		0.398
(0.807) 		0.775
(1.00) 		1
(1.00) 		0.388
(0.799) 		0.382
(0.794) 		0.821
(1.00) 		1
(1.00) 		1
(1.00)
1q loss 54 (12%) 395 0.202
(0.622) 		0.364
(0.78) 		0.0925
(0.413) 		0.876
(1.00) 		0.293
(0.716) 		0.0899
(0.41) 		0.312
(0.744) 		0.61
(0.932) 		0.676
(0.959) 		0.147
(0.53) 		0.204
(0.622) 		0.22
(0.638) 		0.0812
(0.385)
2p loss 6 (1%) 443 0.813
(1.00) 		0.691
(0.97) 		0.165
(0.567) 		0.85
(1.00) 		0.851
(1.00) 		0.595
(0.932) 		0.219
(0.638) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.516
(0.889) 		1
(1.00)
2q loss 7 (2%) 442 0.954
(1.00) 		0.663
(0.953) 		0.208
(0.622) 		1
(1.00) 		1
(1.00) 		0.605
(0.932) 		0.126
(0.49) 		1
(1.00) 		0.6
(0.932) 		1
(1.00) 		0.797
(1.00) 		1
(1.00)
3q loss 34 (8%) 415 0.652
(0.946) 		0.601
(0.932) 		0.839
(1.00) 		0.499
(0.875) 		0.91
(1.00) 		0.302
(0.725) 		0.48
(0.86) 		1
(1.00) 		0.605
(0.932) 		0.939
(1.00) 		0.929
(1.00) 		0.521
(0.892) 		1
(1.00)
7q loss 4 (1%) 445 0.372
(0.782) 		0.0995
(0.424) 		0.278
(0.707) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.327
(0.751) 		1
(1.00) 		0.0576
(0.31)
8q loss 25 (6%) 424 0.6
(0.932) 		0.952
(1.00) 		0.0449
(0.26) 		0.558
(0.919) 		0.0654
(0.338) 		0.0929
(0.413) 		0.838
(1.00) 		1
(1.00) 		0.766
(1.00) 		0.254
(0.685) 		0.614
(0.933) 		0.0572
(0.309) 		1
(1.00)
10q loss 72 (16%) 377 0.499
(0.875) 		0.0913
(0.413) 		0.135
(0.508) 		0.867
(1.00) 		0.238
(0.663) 		0.0624
(0.33) 		0.7
(0.978) 		0.214
(0.629) 		0.192
(0.61) 		0.352
(0.768) 		0.15
(0.531) 		0.649
(0.946) 		0.541
(0.911)
16p loss 31 (7%) 418 0.193
(0.611) 		0.136
(0.508) 		0.396
(0.807) 		0.56
(0.919) 		0.686
(0.968) 		0.27
(0.701) 		0.711
(0.983) 		1
(1.00) 		0.416
(0.817) 		0.225
(0.647) 		0.435
(0.831) 		0.257
(0.687) 		0.321
(0.75)
16q loss 28 (6%) 421 0.325
(0.751) 		0.0507
(0.287) 		0.611
(0.932) 		0.761
(1.00) 		0.798
(1.00) 		0.379
(0.791) 		0.846
(1.00) 		1
(1.00) 		0.571
(0.923) 		0.37
(0.782) 		0.607
(0.932) 		0.233
(0.655) 		0.287
(0.716)
20p loss 43 (10%) 406 0.202
(0.622) 		0.448
(0.845) 		0.611
(0.932) 		0.877
(1.00) 		0.568
(0.923) 		0.816
(1.00) 		0.633
(0.939) 		0.607
(0.932) 		0.488
(0.862) 		1
(1.00) 		0.965
(1.00) 		0.812
(1.00) 		0.353
(0.77)
20q loss 4 (1%) 445 0.331
(0.751) 		0.246
(0.676) 		0.464
(0.857) 		0.782
(1.00) 		0.127
(0.49) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.161
(0.557) 		1
(1.00)
'1q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00727 (Fisher's exact test), Q value = 0.095

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

nPatients 0 1
ALL 328 64
1Q GAIN MUTATED 52 20
1Q GAIN WILD-TYPE 276 44

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

'1q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0201 (Wilcoxon-test), Q value = 0.16

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

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
1Q GAIN MUTATED 77 2.8 (4.5)
1Q GAIN WILD-TYPE 347 1.9 (4.4)

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

'3p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.003 (Fisher's exact test), Q value = 0.06

Table S3.  Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
3P GAIN MUTATED 6 1 2 11 1 0 3 3 2 7 5 1 2
3P GAIN WILD-TYPE 68 0 27 121 9 1 17 5 57 34 40 16 0

Figure S3.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00562 (Fisher's exact test), Q value = 0.079

Table S4.  Gene #6: '3q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
3Q GAIN MUTATED 8 1 4 13 1 0 4 4 5 8 8 3 2
3Q GAIN WILD-TYPE 66 0 25 119 9 1 16 4 54 33 37 14 0

Figure S4.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0263 (Fisher's exact test), Q value = 0.19

Table S5.  Gene #7: '4p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
4P GAIN MUTATED 3 4 5
4P GAIN WILD-TYPE 259 101 77

Figure S5.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0152 (Wilcoxon-test), Q value = 0.14

Table S6.  Gene #7: '4p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
4P GAIN MUTATED 12 3.4 (3.7)
4P GAIN WILD-TYPE 412 2.0 (4.5)

Figure S6.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'4p gain' versus 'RACE'

P value = 0.00361 (Fisher's exact test), Q value = 0.068

Table S7.  Gene #7: '4p gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 59 212
4P GAIN MUTATED 1 0 5 4
4P GAIN WILD-TYPE 0 11 54 208

Figure S7.  Get High-res Image Gene #7: '4p gain' versus Clinical Feature #12: 'RACE'

'4q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00252 (Fisher's exact test), Q value = 0.052

Table S8.  Gene #8: '4q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
4Q GAIN MUTATED 4 5 8
4Q GAIN WILD-TYPE 258 100 74

Figure S8.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q gain' versus 'PATHOLOGY_M_STAGE'

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

Table S9.  Gene #8: '4q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
4Q GAIN MUTATED 8 6
4Q GAIN WILD-TYPE 320 58

Figure S9.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00165 (Wilcoxon-test), Q value = 0.039

Table S10.  Gene #8: '4q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
4Q GAIN MUTATED 17 3.4 (3.2)
4Q GAIN WILD-TYPE 407 2.0 (4.5)

Figure S10.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'4q gain' versus 'RACE'

P value = 0.0325 (Fisher's exact test), Q value = 0.22

Table S11.  Gene #8: '4q gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 59 212
4Q GAIN MUTATED 1 0 4 7
4Q GAIN WILD-TYPE 0 11 55 205

Figure S11.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #12: 'RACE'

'5p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0154 (Fisher's exact test), Q value = 0.14

Table S12.  Gene #9: '5p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
5P GAIN MUTATED 29 21 18
5P GAIN WILD-TYPE 233 84 64

Figure S12.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0095 (Wilcoxon-test), Q value = 0.11

Table S13.  Gene #9: '5p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
5P GAIN MUTATED 66 2.9 (4.5)
5P GAIN WILD-TYPE 358 1.9 (4.4)

Figure S13.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'6p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0304 (Fisher's exact test), Q value = 0.21

Table S14.  Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
6P GAIN MUTATED 42 18 24
6P GAIN WILD-TYPE 220 87 58

Figure S14.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0352 (Wilcoxon-test), Q value = 0.23

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

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
6P GAIN MUTATED 82 3.0 (4.9)
6P GAIN WILD-TYPE 342 1.9 (4.3)

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

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0354 (Fisher's exact test), Q value = 0.23

Table S16.  Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
6Q GAIN MUTATED 38 16 22
6Q GAIN WILD-TYPE 224 89 60

Figure S16.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'PATHOLOGIC_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0058

Table S17.  Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
7P GAIN MUTATED 40 1 15 51 2 0 12 8 39 26 30 12 1
7P GAIN WILD-TYPE 34 0 14 81 8 1 8 0 20 15 15 5 1

Figure S17.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0097

Table S18.  Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
7P GAIN MUTATED 121 72 52
7P GAIN WILD-TYPE 141 33 30

Figure S18.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0197 (Fisher's exact test), Q value = 0.16

Table S19.  Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
7P GAIN MUTATED 167 43
7P GAIN WILD-TYPE 161 21

Figure S19.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0189 (Fisher's exact test), Q value = 0.16

Table S20.  Gene #13: '7p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
7P GAIN MUTATED 218 25
7P GAIN WILD-TYPE 164 37

Figure S20.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000584 (Wilcoxon-test), Q value = 0.021

Table S21.  Gene #13: '7p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
7P GAIN MUTATED 236 2.4 (4.8)
7P GAIN WILD-TYPE 188 1.7 (4.0)

Figure S21.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'7q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0109 (Fisher's exact test), Q value = 0.12

Table S22.  Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
7Q GAIN MUTATED 38 1 14 47 2 0 11 5 34 23 27 12 1
7Q GAIN WILD-TYPE 36 0 15 85 8 1 9 3 25 18 18 5 1

Figure S22.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0123 (Fisher's exact test), Q value = 0.13

Table S23.  Gene #14: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
7Q GAIN MUTATED 114 61 47
7Q GAIN WILD-TYPE 148 44 35

Figure S23.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0139 (Fisher's exact test), Q value = 0.13

Table S24.  Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
7Q GAIN MUTATED 149 40
7Q GAIN WILD-TYPE 179 24

Figure S24.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0406 (Fisher's exact test), Q value = 0.25

Table S25.  Gene #14: '7q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
7Q GAIN MUTATED 196 23
7Q GAIN WILD-TYPE 186 39

Figure S25.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0128 (Wilcoxon-test), Q value = 0.13

Table S26.  Gene #14: '7q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
7Q GAIN MUTATED 215 2.3 (4.8)
7Q GAIN WILD-TYPE 209 1.8 (4.0)

Figure S26.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'8q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0343 (Wilcoxon-test), Q value = 0.23

Table S27.  Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 447 66.9 (13.1)
8Q GAIN MUTATED 225 65.8 (12.6)
8Q GAIN WILD-TYPE 222 68.0 (13.4)

Figure S27.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8q gain' versus 'HISTOLOGICAL_TYPE'

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

Table S28.  Gene #16: '8q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
8Q GAIN MUTATED 202 22
8Q GAIN WILD-TYPE 180 40

Figure S28.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'9p gain' versus 'Time to Death'

P value = 0.00621 (logrank test), Q value = 0.086

Table S29.  Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 436 101 0.0 - 148.0 (22.0)
9P GAIN MUTATED 79 27 0.0 - 98.2 (17.9)
9P GAIN WILD-TYPE 357 74 0.0 - 148.0 (23.1)

Figure S29.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0194 (Fisher's exact test), Q value = 0.16

Table S30.  Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
9P GAIN MUTATED 9 1 6 18 3 0 1 3 8 13 9 5 1
9P GAIN WILD-TYPE 65 0 23 114 7 1 19 5 51 28 36 12 1

Figure S30.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0218 (Fisher's exact test), Q value = 0.17

Table S31.  Gene #17: '9p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
9P GAIN MUTATED 63 18
9P GAIN WILD-TYPE 319 44

Figure S31.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'9p gain' versus 'RACE'

P value = 0.0163 (Fisher's exact test), Q value = 0.14

Table S32.  Gene #17: '9p gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 59 212
9P GAIN MUTATED 1 1 18 35
9P GAIN WILD-TYPE 0 10 41 177

Figure S32.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #12: 'RACE'

'9q gain' versus 'Time to Death'

P value = 0.00994 (logrank test), Q value = 0.11

Table S33.  Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 436 101 0.0 - 148.0 (22.0)
9Q GAIN MUTATED 69 24 0.0 - 98.2 (17.0)
9Q GAIN WILD-TYPE 367 77 0.0 - 148.0 (23.5)

Figure S33.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #1: 'Time to Death'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0378 (Fisher's exact test), Q value = 0.24

Table S34.  Gene #18: '9q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
9Q GAIN MUTATED 55 16
9Q GAIN WILD-TYPE 327 46

Figure S34.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10q gain' versus 'RACE'

P value = 0.0197 (Fisher's exact test), Q value = 0.16

Table S35.  Gene #20: '10q gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 59 212
10Q GAIN MUTATED 1 1 6 10
10Q GAIN WILD-TYPE 0 10 53 202

Figure S35.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #12: 'RACE'

'10q gain' versus 'ETHNICITY'

P value = 0.0181 (Fisher's exact test), Q value = 0.15

Table S36.  Gene #20: '10q gain' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 4 269
10Q GAIN MUTATED 2 14
10Q GAIN WILD-TYPE 2 255

Figure S36.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #13: 'ETHNICITY'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0133 (Wilcoxon-test), Q value = 0.13

Table S37.  Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 447 66.9 (13.1)
11P GAIN MUTATED 54 62.6 (13.5)
11P GAIN WILD-TYPE 393 67.5 (12.9)

Figure S37.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0245 (Fisher's exact test), Q value = 0.18

Table S38.  Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
11P GAIN MUTATED 6 0 2 8 1 0 1 3 9 7 9 5 0
11P GAIN WILD-TYPE 68 1 27 124 9 1 19 5 50 34 36 12 2

Figure S38.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p gain' versus 'PATHOLOGY_N_STAGE'

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

Table S39.  Gene #21: '11p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
11P GAIN MUTATED 22 17 15
11P GAIN WILD-TYPE 240 88 67

Figure S39.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00868 (Fisher's exact test), Q value = 0.11

Table S40.  Gene #21: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
11P GAIN MUTATED 31 14
11P GAIN WILD-TYPE 297 50

Figure S40.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0194 (Fisher's exact test), Q value = 0.16

Table S41.  Gene #21: '11p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
11P GAIN MUTATED 51 2
11P GAIN WILD-TYPE 331 60

Figure S41.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0147 (Wilcoxon-test), Q value = 0.14

Table S42.  Gene #21: '11p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
11P GAIN MUTATED 53 3.4 (7.4)
11P GAIN WILD-TYPE 371 1.9 (3.8)

Figure S42.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000379 (Wilcoxon-test), Q value = 0.017

Table S43.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 447 66.9 (13.1)
11Q GAIN MUTATED 51 60.5 (13.2)
11Q GAIN WILD-TYPE 396 67.7 (12.8)

Figure S43.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0187 (Fisher's exact test), Q value = 0.16

Table S44.  Gene #22: '11q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
11Q GAIN MUTATED 5 0 3 7 1 0 1 3 9 8 6 5 0
11Q GAIN WILD-TYPE 69 1 26 125 9 1 19 5 50 33 39 12 2

Figure S44.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0114 (Fisher's exact test), Q value = 0.13

Table S45.  Gene #22: '11q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
11Q GAIN MUTATED 20 17 14
11Q GAIN WILD-TYPE 242 88 68

Figure S45.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00467 (Fisher's exact test), Q value = 0.076

Table S46.  Gene #22: '11q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
11Q GAIN MUTATED 50 1
11Q GAIN WILD-TYPE 332 61

Figure S46.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'NUMBER_OF_LYMPH_NODES'

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

Table S47.  Gene #22: '11q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
11Q GAIN MUTATED 50 3.3 (7.4)
11Q GAIN WILD-TYPE 374 1.9 (3.9)

Figure S47.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'12q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0168 (Fisher's exact test), Q value = 0.15

Table S48.  Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
12Q GAIN MUTATED 12 1 7 36 2 0 3 3 6 8 3 6 0
12Q GAIN WILD-TYPE 62 0 22 96 8 1 17 5 53 33 42 11 2

Figure S48.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0368 (Fisher's exact test), Q value = 0.24

Table S49.  Gene #24: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
12Q GAIN MUTATED 61 18 9
12Q GAIN WILD-TYPE 201 87 73

Figure S49.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0149 (Wilcoxon-test), Q value = 0.14

Table S50.  Gene #24: '12q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
12Q GAIN MUTATED 84 1.1 (2.0)
12Q GAIN WILD-TYPE 340 2.3 (4.8)

Figure S50.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'13q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00152 (Fisher's exact test), Q value = 0.037

Table S51.  Gene #25: '13q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
13Q GAIN MUTATED 41 0 15 62 3 1 11 8 35 25 35 12 0
13Q GAIN WILD-TYPE 33 1 14 70 7 0 9 0 24 16 10 5 2

Figure S51.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'13q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00495 (Fisher's exact test), Q value = 0.079

Table S52.  Gene #25: '13q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
13Q GAIN MUTATED 132 69 54
13Q GAIN WILD-TYPE 130 36 28

Figure S52.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'13q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00555 (Fisher's exact test), Q value = 0.079

Table S53.  Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
13Q GAIN MUTATED 179 47
13Q GAIN WILD-TYPE 149 17

Figure S53.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 6.79e-07 (Fisher's exact test), Q value = 0.00012

Table S54.  Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
13Q GAIN MUTATED 236 17
13Q GAIN WILD-TYPE 146 45

Figure S54.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'13q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0329 (Fisher's exact test), Q value = 0.22

Table S55.  Gene #25: '13q gain' versus Clinical Feature #10: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 323 4 25 25
13Q GAIN MUTATED 177 2 19 9
13Q GAIN WILD-TYPE 146 2 6 16

Figure S55.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #10: 'RESIDUAL_TUMOR'

'13q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00961 (Wilcoxon-test), Q value = 0.11

Table S56.  Gene #25: '13q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
13Q GAIN MUTATED 248 2.2 (3.9)
13Q GAIN WILD-TYPE 176 1.9 (5.1)

Figure S56.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'14q gain' versus 'RACE'

P value = 0.0229 (Fisher's exact test), Q value = 0.17

Table S57.  Gene #26: '14q gain' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 59 212
14Q GAIN MUTATED 1 2 2 19
14Q GAIN WILD-TYPE 0 9 57 193

Figure S57.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #12: 'RACE'

'16p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0046 (Fisher's exact test), Q value = 0.076

Table S58.  Gene #28: '16p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
16P GAIN MUTATED 12 1 3 25 1 0 7 6 13 14 13 4 1
16P GAIN WILD-TYPE 62 0 26 107 9 1 13 2 46 27 32 13 1

Figure S58.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'16p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00687 (Fisher's exact test), Q value = 0.092

Table S59.  Gene #28: '16p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
16P GAIN MUTATED 48 32 26
16P GAIN WILD-TYPE 214 73 56

Figure S59.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00116 (Fisher's exact test), Q value = 0.032

Table S60.  Gene #28: '16p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
16P GAIN MUTATED 99 5
16P GAIN WILD-TYPE 283 57

Figure S60.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00542 (Wilcoxon-test), Q value = 0.079

Table S61.  Gene #28: '16p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
16P GAIN MUTATED 101 2.6 (4.0)
16P GAIN WILD-TYPE 323 1.9 (4.6)

Figure S61.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'16q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00104 (Fisher's exact test), Q value = 0.031

Table S62.  Gene #29: '16q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
16Q GAIN MUTATED 12 1 3 23 1 0 7 7 16 12 11 4 1
16Q GAIN WILD-TYPE 62 0 26 109 9 1 13 1 43 29 34 13 1

Figure S62.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'16q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00363 (Fisher's exact test), Q value = 0.068

Table S63.  Gene #29: '16q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
16Q GAIN MUTATED 46 33 25
16Q GAIN WILD-TYPE 216 72 57

Figure S63.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00177 (Fisher's exact test), Q value = 0.041

Table S64.  Gene #29: '16q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
16Q GAIN MUTATED 97 5
16Q GAIN WILD-TYPE 285 57

Figure S64.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'16q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00524 (Wilcoxon-test), Q value = 0.079

Table S65.  Gene #29: '16q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
16Q GAIN MUTATED 100 2.6 (4.1)
16Q GAIN WILD-TYPE 324 1.9 (4.5)

Figure S65.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'17q gain' versus 'ETHNICITY'

P value = 0.0282 (Fisher's exact test), Q value = 0.2

Table S66.  Gene #31: '17q gain' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 4 269
17Q GAIN MUTATED 3 53
17Q GAIN WILD-TYPE 1 216

Figure S66.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #13: 'ETHNICITY'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0291 (Fisher's exact test), Q value = 0.21

Table S67.  Gene #32: '18p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
18P GAIN MUTATED 16 7
18P GAIN WILD-TYPE 366 55

Figure S67.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0331 (Fisher's exact test), Q value = 0.22

Table S68.  Gene #33: '18q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
18Q GAIN MUTATED 9 5
18Q GAIN WILD-TYPE 373 57

Figure S68.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00384 (Fisher's exact test), Q value = 0.069

Table S69.  Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
20P GAIN MUTATED 41 1 14 62 3 0 9 8 28 22 33 13 1
20P GAIN WILD-TYPE 33 0 15 70 7 1 11 0 31 19 12 4 1

Figure S69.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.000936 (Fisher's exact test), Q value = 0.029

Table S70.  Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
20P GAIN MUTATED 167 47
20P GAIN WILD-TYPE 161 17

Figure S70.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.000323 (Fisher's exact test), Q value = 0.016

Table S71.  Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
20P GAIN MUTATED 218 20
20P GAIN WILD-TYPE 164 42

Figure S71.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.013 (Fisher's exact test), Q value = 0.13

Table S72.  Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
20Q GAIN MUTATED 53 1 17 85 4 1 13 8 42 32 39 15 1
20Q GAIN WILD-TYPE 21 0 12 47 6 0 7 0 17 9 6 2 1

Figure S72.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0168 (Fisher's exact test), Q value = 0.15

Table S73.  Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
20Q GAIN MUTATED 173 84 62
20Q GAIN WILD-TYPE 89 21 20

Figure S73.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00404 (Fisher's exact test), Q value = 0.071

Table S74.  Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
20Q GAIN MUTATED 225 55
20Q GAIN WILD-TYPE 103 9

Figure S74.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 2.72e-07 (Fisher's exact test), Q value = 8.9e-05

Table S75.  Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
20Q GAIN MUTATED 289 26
20Q GAIN WILD-TYPE 93 36

Figure S75.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0255 (Wilcoxon-test), Q value = 0.19

Table S76.  Gene #37: '20q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
20Q GAIN MUTATED 304 2.3 (4.8)
20Q GAIN WILD-TYPE 120 1.6 (3.4)

Figure S76.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00186 (Wilcoxon-test), Q value = 0.041

Table S77.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 447 66.9 (13.1)
21Q GAIN MUTATED 24 59.8 (10.0)
21Q GAIN WILD-TYPE 423 67.3 (13.1)

Figure S77.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0179 (Fisher's exact test), Q value = 0.15

Table S78.  Gene #40: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 11 77 305 55
XP GAIN MUTATED 0 13 53 2
XP GAIN WILD-TYPE 11 64 252 53

Figure S78.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00384 (Fisher's exact test), Q value = 0.069

Table S79.  Gene #41: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 11 77 305 55
XQ GAIN MUTATED 0 14 63 2
XQ GAIN WILD-TYPE 11 63 242 53

Figure S79.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1p loss' versus 'Time to Death'

P value = 0.00763 (logrank test), Q value = 0.096

Table S80.  Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 436 101 0.0 - 148.0 (22.0)
1P LOSS MUTATED 88 28 1.6 - 92.8 (20.9)
1P LOSS WILD-TYPE 348 73 0.0 - 148.0 (22.2)

Figure S80.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #1: 'Time to Death'

'1p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00894 (Fisher's exact test), Q value = 0.11

Table S81.  Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
1P LOSS MUTATED 8 0 3 24 1 0 5 3 9 12 19 4 0
1P LOSS WILD-TYPE 66 1 26 108 9 1 15 5 50 29 26 13 2

Figure S81.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00188 (Fisher's exact test), Q value = 0.041

Table S82.  Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
1P LOSS MUTATED 41 23 28
1P LOSS WILD-TYPE 221 82 54

Figure S82.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00205 (Fisher's exact test), Q value = 0.044

Table S83.  Gene #42: '1p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
1P LOSS MUTATED 58 23
1P LOSS WILD-TYPE 270 41

Figure S83.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'1p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000702 (Wilcoxon-test), Q value = 0.024

Table S84.  Gene #42: '1p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
1P LOSS MUTATED 86 3.7 (6.9)
1P LOSS WILD-TYPE 338 1.7 (3.5)

Figure S84.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'3p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0343 (Fisher's exact test), Q value = 0.23

Table S85.  Gene #46: '3p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
3P LOSS MUTATED 34 13
3P LOSS WILD-TYPE 294 51

Figure S85.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00256 (Fisher's exact test), Q value = 0.052

Table S86.  Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
4P LOSS MUTATED 16 0 6 35 3 0 5 5 14 15 26 7 1
4P LOSS WILD-TYPE 58 1 23 97 7 1 15 3 45 26 19 10 1

Figure S86.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00466 (Fisher's exact test), Q value = 0.076

Table S87.  Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
4P LOSS MUTATED 65 37 35
4P LOSS WILD-TYPE 197 68 47

Figure S87.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'PATHOLOGY_M_STAGE'

P value = 2.45e-05 (Fisher's exact test), Q value = 0.0037

Table S88.  Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
4P LOSS MUTATED 84 34
4P LOSS WILD-TYPE 244 30

Figure S88.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00726 (Fisher's exact test), Q value = 0.095

Table S89.  Gene #48: '4p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
4P LOSS MUTATED 126 10
4P LOSS WILD-TYPE 256 52

Figure S89.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'4p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00154 (Wilcoxon-test), Q value = 0.037

Table S90.  Gene #48: '4p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
4P LOSS MUTATED 131 2.9 (4.7)
4P LOSS WILD-TYPE 293 1.7 (4.3)

Figure S90.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'4q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0203 (Fisher's exact test), Q value = 0.16

Table S91.  Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
4Q LOSS MUTATED 14 0 5 33 2 0 4 5 16 17 21 5 0
4Q LOSS WILD-TYPE 60 1 24 99 8 1 16 3 43 24 24 12 2

Figure S91.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00521 (Fisher's exact test), Q value = 0.079

Table S92.  Gene #49: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
4Q LOSS MUTATED 58 36 31
4Q LOSS WILD-TYPE 204 69 51

Figure S92.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0135 (Fisher's exact test), Q value = 0.13

Table S93.  Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
4Q LOSS MUTATED 81 26
4Q LOSS WILD-TYPE 247 38

Figure S93.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00225 (Wilcoxon-test), Q value = 0.047

Table S94.  Gene #49: '4q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
4Q LOSS MUTATED 119 2.9 (4.7)
4Q LOSS WILD-TYPE 305 1.8 (4.3)

Figure S94.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0151 (Fisher's exact test), Q value = 0.14

Table S95.  Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
5P LOSS MUTATED 9 0 4 10 0 1 2 3 10 9 5 6 0
5P LOSS WILD-TYPE 65 1 25 122 10 0 18 5 49 32 40 11 2

Figure S95.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p loss' versus 'ETHNICITY'

P value = 0.0106 (Fisher's exact test), Q value = 0.12

Table S96.  Gene #50: '5p loss' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 4 269
5P LOSS MUTATED 3 37
5P LOSS WILD-TYPE 1 232

Figure S96.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #13: 'ETHNICITY'

'5q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0362 (Fisher's exact test), Q value = 0.23

Table S97.  Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
5Q LOSS MUTATED 11 0 4 16 0 0 2 3 11 14 11 6 0
5Q LOSS WILD-TYPE 63 1 25 116 10 1 18 5 48 27 34 11 2

Figure S97.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00377 (Fisher's exact test), Q value = 0.069

Table S98.  Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
5Q LOSS MUTATED 36 19 25
5Q LOSS WILD-TYPE 226 86 57

Figure S98.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00113 (Wilcoxon-test), Q value = 0.032

Table S99.  Gene #51: '5q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
5Q LOSS MUTATED 76 3.5 (5.6)
5Q LOSS WILD-TYPE 348 1.8 (4.1)

Figure S99.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'5q loss' versus 'ETHNICITY'

P value = 0.0228 (Fisher's exact test), Q value = 0.17

Table S100.  Gene #51: '5q loss' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 4 269
5Q LOSS MUTATED 3 49
5Q LOSS WILD-TYPE 1 220

Figure S100.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #13: 'ETHNICITY'

'6p loss' versus 'Time to Death'

P value = 0.0384 (logrank test), Q value = 0.24

Table S101.  Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 436 101 0.0 - 148.0 (22.0)
6P LOSS MUTATED 32 10 2.0 - 45.4 (17.9)
6P LOSS WILD-TYPE 404 91 0.0 - 148.0 (22.5)

Figure S101.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'RACE'

P value = 0.0294 (Fisher's exact test), Q value = 0.21

Table S102.  Gene #52: '6p loss' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 59 212
6P LOSS MUTATED 0 3 1 17
6P LOSS WILD-TYPE 1 8 58 195

Figure S102.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #12: 'RACE'

'6q loss' versus 'Time to Death'

P value = 0.0188 (logrank test), Q value = 0.16

Table S103.  Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 436 101 0.0 - 148.0 (22.0)
6Q LOSS MUTATED 44 13 0.5 - 61.0 (14.5)
6Q LOSS WILD-TYPE 392 88 0.0 - 148.0 (23.0)

Figure S103.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00669 (Wilcoxon-test), Q value = 0.09

Table S104.  Gene #53: '6q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
6Q LOSS MUTATED 40 3.2 (4.3)
6Q LOSS WILD-TYPE 384 2.0 (4.5)

Figure S104.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'6q loss' versus 'RACE'

P value = 0.0129 (Fisher's exact test), Q value = 0.13

Table S105.  Gene #53: '6q loss' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 59 212
6Q LOSS MUTATED 1 3 3 19
6Q LOSS WILD-TYPE 0 8 56 193

Figure S105.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #12: 'RACE'

'8p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00749 (Fisher's exact test), Q value = 0.095

Table S106.  Gene #55: '8p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
8P LOSS MUTATED 15 0 7 31 2 0 7 4 17 18 22 9 1
8P LOSS WILD-TYPE 59 1 22 101 8 1 13 4 42 23 23 8 1

Figure S106.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00052 (Fisher's exact test), Q value = 0.021

Table S107.  Gene #55: '8p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
8P LOSS MUTATED 62 37 37
8P LOSS WILD-TYPE 200 68 45

Figure S107.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000571 (Fisher's exact test), Q value = 0.021

Table S108.  Gene #55: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
8P LOSS MUTATED 89 32
8P LOSS WILD-TYPE 239 32

Figure S108.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0247 (Fisher's exact test), Q value = 0.18

Table S109.  Gene #55: '8p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
8P LOSS MUTATED 123 11
8P LOSS WILD-TYPE 259 51

Figure S109.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000222 (Wilcoxon-test), Q value = 0.013

Table S110.  Gene #55: '8p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
8P LOSS MUTATED 132 3.1 (5.9)
8P LOSS WILD-TYPE 292 1.6 (3.5)

Figure S110.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00469 (Fisher's exact test), Q value = 0.076

Table S111.  Gene #57: '9p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
9P LOSS MUTATED 51 1
9P LOSS WILD-TYPE 331 61

Figure S111.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00467 (Fisher's exact test), Q value = 0.076

Table S112.  Gene #58: '9q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
9Q LOSS MUTATED 50 1
9Q LOSS WILD-TYPE 332 61

Figure S112.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'10p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0397 (Fisher's exact test), Q value = 0.24

Table S113.  Gene #59: '10p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
10P LOSS MUTATED 10 0 6 11 1 1 1 2 10 7 12 3 1
10P LOSS WILD-TYPE 64 1 23 121 9 0 19 6 49 34 33 14 1

Figure S113.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'10p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0195 (Fisher's exact test), Q value = 0.16

Table S114.  Gene #59: '10p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
10P LOSS MUTATED 42 16
10P LOSS WILD-TYPE 286 48

Figure S114.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0371 (Fisher's exact test), Q value = 0.24

Table S115.  Gene #61: '11p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
11P LOSS MUTATED 21 17 12
11P LOSS WILD-TYPE 241 88 70

Figure S115.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00906 (Wilcoxon-test), Q value = 0.11

Table S116.  Gene #61: '11p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
11P LOSS MUTATED 47 3.0 (4.7)
11P LOSS WILD-TYPE 377 2.0 (4.4)

Figure S116.  Get High-res Image Gene #61: '11p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'11q loss' versus 'PATHOLOGY_M_STAGE'

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

Table S117.  Gene #62: '11q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
11Q LOSS MUTATED 38 15
11Q LOSS WILD-TYPE 290 49

Figure S117.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0411 (Wilcoxon-test), Q value = 0.25

Table S118.  Gene #62: '11q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
11Q LOSS MUTATED 59 2.5 (4.3)
11Q LOSS WILD-TYPE 365 2.0 (4.5)

Figure S118.  Get High-res Image Gene #62: '11q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'12p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00741 (Fisher's exact test), Q value = 0.095

Table S119.  Gene #63: '12p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
12P LOSS MUTATED 47 1
12P LOSS WILD-TYPE 335 61

Figure S119.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0327 (Wilcoxon-test), Q value = 0.22

Table S120.  Gene #63: '12p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
12P LOSS MUTATED 46 2.5 (3.7)
12P LOSS WILD-TYPE 378 2.0 (4.5)

Figure S120.  Get High-res Image Gene #63: '12p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'12q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0349 (Fisher's exact test), Q value = 0.23

Table S121.  Gene #64: '12q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
12Q LOSS MUTATED 21 15 14
12Q LOSS WILD-TYPE 241 90 68

Figure S121.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0294 (Fisher's exact test), Q value = 0.21

Table S122.  Gene #64: '12q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
12Q LOSS MUTATED 48 2
12Q LOSS WILD-TYPE 334 60

Figure S122.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'12q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0115 (Wilcoxon-test), Q value = 0.13

Table S123.  Gene #64: '12q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
12Q LOSS MUTATED 47 2.7 (3.8)
12Q LOSS WILD-TYPE 377 2.0 (4.5)

Figure S123.  Get High-res Image Gene #64: '12q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0129 (Wilcoxon-test), Q value = 0.13

Table S124.  Gene #65: '13q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
13Q LOSS MUTATED 9 10.6 (15.8)
13Q LOSS WILD-TYPE 415 1.9 (3.7)

Figure S124.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'RACE'

P value = 0.0191 (Fisher's exact test), Q value = 0.16

Table S125.  Gene #65: '13q loss' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 11 59 212
13Q LOSS MUTATED 1 1 1 6
13Q LOSS WILD-TYPE 0 10 58 206

Figure S125.  Get High-res Image Gene #65: '13q loss' versus Clinical Feature #12: 'RACE'

'14q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0116 (Fisher's exact test), Q value = 0.13

Table S126.  Gene #66: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
14Q LOSS MUTATED 93 29
14Q LOSS WILD-TYPE 235 35

Figure S126.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 3.4e-07 (Fisher's exact test), Q value = 8.9e-05

Table S127.  Gene #66: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
14Q LOSS MUTATED 130 3
14Q LOSS WILD-TYPE 252 59

Figure S127.  Get High-res Image Gene #66: '14q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0382 (Fisher's exact test), Q value = 0.24

Table S128.  Gene #67: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
15Q LOSS MUTATED 79 43 35
15Q LOSS WILD-TYPE 183 62 47

Figure S128.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000946 (Fisher's exact test), Q value = 0.029

Table S129.  Gene #67: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
15Q LOSS MUTATED 102 34
15Q LOSS WILD-TYPE 226 30

Figure S129.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0145 (Fisher's exact test), Q value = 0.14

Table S130.  Gene #67: '15q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
15Q LOSS MUTATED 141 13
15Q LOSS WILD-TYPE 241 49

Figure S130.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'15q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0199 (Wilcoxon-test), Q value = 0.16

Table S131.  Gene #67: '15q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
15Q LOSS MUTATED 148 2.3 (3.8)
15Q LOSS WILD-TYPE 276 1.9 (4.7)

Figure S131.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'17p loss' versus 'PATHOLOGIC_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0063

Table S132.  Gene #70: '17p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
17P LOSS MUTATED 32 0 14 55 2 1 10 8 30 27 33 12 2
17P LOSS WILD-TYPE 42 1 15 77 8 0 10 0 29 14 12 5 0

Figure S132.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 3e-04 (Fisher's exact test), Q value = 0.016

Table S133.  Gene #70: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
17P LOSS MUTATED 116 64 54
17P LOSS WILD-TYPE 146 41 28

Figure S133.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000329 (Fisher's exact test), Q value = 0.016

Table S134.  Gene #70: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
17P LOSS MUTATED 160 47
17P LOSS WILD-TYPE 168 17

Figure S134.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17p loss' versus 'GENDER'

P value = 0.0381 (Fisher's exact test), Q value = 0.24

Table S135.  Gene #70: '17p loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 213 236
17P LOSS MUTATED 100 134
17P LOSS WILD-TYPE 113 102

Figure S135.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #7: 'GENDER'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 5.27e-07 (Fisher's exact test), Q value = 0.00011

Table S136.  Gene #70: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
17P LOSS MUTATED 216 14
17P LOSS WILD-TYPE 166 48

Figure S136.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 7.47e-05 (Wilcoxon-test), Q value = 0.0072

Table S137.  Gene #70: '17p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
17P LOSS MUTATED 221 2.7 (5.5)
17P LOSS WILD-TYPE 203 1.4 (2.8)

Figure S137.  Get High-res Image Gene #70: '17p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'17q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00651 (Fisher's exact test), Q value = 0.089

Table S138.  Gene #71: '17q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
17Q LOSS MUTATED 26 20 18
17Q LOSS WILD-TYPE 236 85 64

Figure S138.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0235 (Fisher's exact test), Q value = 0.18

Table S139.  Gene #71: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
17Q LOSS MUTATED 36 14
17Q LOSS WILD-TYPE 292 50

Figure S139.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000339 (Wilcoxon-test), Q value = 0.016

Table S140.  Gene #71: '17q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
17Q LOSS MUTATED 60 3.8 (7.3)
17Q LOSS WILD-TYPE 364 1.8 (3.7)

Figure S140.  Get High-res Image Gene #71: '17q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'18p loss' versus 'YEARS_TO_BIRTH'

P value = 0.023 (Wilcoxon-test), Q value = 0.17

Table S141.  Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 447 66.9 (13.1)
18P LOSS MUTATED 251 65.9 (12.3)
18P LOSS WILD-TYPE 196 68.2 (13.9)

Figure S141.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00095 (Fisher's exact test), Q value = 0.029

Table S142.  Gene #72: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
18P LOSS MUTATED 37 0 12 66 3 1 8 6 35 25 35 15 1
18P LOSS WILD-TYPE 37 1 17 66 7 0 12 2 24 16 10 2 1

Figure S142.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0121 (Fisher's exact test), Q value = 0.13

Table S143.  Gene #72: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
18P LOSS MUTATED 131 68 52
18P LOSS WILD-TYPE 131 37 30

Figure S143.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18p loss' versus 'PATHOLOGY_M_STAGE'

P value = 2.92e-05 (Fisher's exact test), Q value = 0.0038

Table S144.  Gene #72: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
18P LOSS MUTATED 170 51
18P LOSS WILD-TYPE 158 13

Figure S144.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 8e-11 (Fisher's exact test), Q value = 8.4e-08

Table S145.  Gene #72: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
18P LOSS MUTATED 236 11
18P LOSS WILD-TYPE 146 51

Figure S145.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00527 (Wilcoxon-test), Q value = 0.079

Table S146.  Gene #72: '18p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
18P LOSS MUTATED 237 2.4 (5.1)
18P LOSS WILD-TYPE 187 1.6 (3.4)

Figure S146.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'18q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0118 (Wilcoxon-test), Q value = 0.13

Table S147.  Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 447 66.9 (13.1)
18Q LOSS MUTATED 267 65.8 (12.4)
18Q LOSS WILD-TYPE 180 68.5 (13.9)

Figure S147.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00048 (Fisher's exact test), Q value = 0.02

Table S148.  Gene #73: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
18Q LOSS MUTATED 37 0 15 69 3 1 10 7 37 28 36 15 1
18Q LOSS WILD-TYPE 37 1 14 63 7 0 10 1 22 13 9 2 1

Figure S148.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00127 (Fisher's exact test), Q value = 0.033

Table S149.  Gene #73: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
18Q LOSS MUTATED 137 73 57
18Q LOSS WILD-TYPE 125 32 25

Figure S149.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000145 (Fisher's exact test), Q value = 0.011

Table S150.  Gene #73: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
18Q LOSS MUTATED 185 52
18Q LOSS WILD-TYPE 143 12

Figure S150.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 3.46e-10 (Fisher's exact test), Q value = 1.8e-07

Table S151.  Gene #73: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
18Q LOSS MUTATED 250 14
18Q LOSS WILD-TYPE 132 48

Figure S151.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'18q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00108 (Wilcoxon-test), Q value = 0.032

Table S152.  Gene #73: '18q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
18Q LOSS MUTATED 253 2.4 (4.6)
18Q LOSS WILD-TYPE 171 1.7 (4.1)

Figure S152.  Get High-res Image Gene #73: '18q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'19p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00551 (Fisher's exact test), Q value = 0.079

Table S153.  Gene #74: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
19P LOSS MUTATED 7 0 1 5 1 0 4 0 2 7 7 4 1
19P LOSS WILD-TYPE 67 1 28 127 9 1 16 8 57 34 38 13 1

Figure S153.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00142 (Fisher's exact test), Q value = 0.036

Table S154.  Gene #74: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
19P LOSS MUTATED 15 9 16
19P LOSS WILD-TYPE 247 96 66

Figure S154.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00553 (Fisher's exact test), Q value = 0.079

Table S155.  Gene #74: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
19P LOSS MUTATED 22 12
19P LOSS WILD-TYPE 306 52

Figure S155.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000156 (Wilcoxon-test), Q value = 0.011

Table S156.  Gene #74: '19p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
19P LOSS MUTATED 38 4.3 (5.3)
19P LOSS WILD-TYPE 386 1.9 (4.3)

Figure S156.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'19q loss' versus 'PATHOLOGIC_STAGE'

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

Table S157.  Gene #75: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
19Q LOSS MUTATED 6 0 1 5 0 0 4 0 1 6 5 3 1
19Q LOSS WILD-TYPE 68 1 28 127 10 1 16 8 58 35 40 14 1

Figure S157.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00064 (Fisher's exact test), Q value = 0.022

Table S158.  Gene #75: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
19Q LOSS MUTATED 13 5 15
19Q LOSS WILD-TYPE 249 100 67

Figure S158.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0302 (Fisher's exact test), Q value = 0.21

Table S159.  Gene #75: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
19Q LOSS MUTATED 19 9
19Q LOSS WILD-TYPE 309 55

Figure S159.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000533 (Wilcoxon-test), Q value = 0.021

Table S160.  Gene #75: '19q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
19Q LOSS MUTATED 32 4.7 (5.6)
19Q LOSS WILD-TYPE 392 1.9 (4.3)

Figure S160.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.032 (Fisher's exact test), Q value = 0.22

Table S161.  Gene #78: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
21Q LOSS MUTATED 63 28 32
21Q LOSS WILD-TYPE 199 77 50

Figure S161.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00542 (Fisher's exact test), Q value = 0.079

Table S162.  Gene #78: '21q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
21Q LOSS MUTATED 115 8
21Q LOSS WILD-TYPE 267 54

Figure S162.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0387 (Wilcoxon-test), Q value = 0.24

Table S163.  Gene #78: '21q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
21Q LOSS MUTATED 117 3.1 (6.5)
21Q LOSS WILD-TYPE 307 1.7 (3.3)

Figure S163.  Get High-res Image Gene #78: '21q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'22q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.013

Table S164.  Gene #79: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA STAGE IVB
ALL 74 1 29 132 10 1 20 8 59 41 45 17 2
22Q LOSS MUTATED 17 0 8 33 1 0 5 6 16 21 24 8 0
22Q LOSS WILD-TYPE 57 1 21 99 9 1 15 2 43 20 21 9 2

Figure S164.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.011

Table S165.  Gene #79: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
22Q LOSS MUTATED 64 43 37
22Q LOSS WILD-TYPE 198 62 45

Figure S165.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00122 (Fisher's exact test), Q value = 0.033

Table S166.  Gene #79: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
22Q LOSS MUTATED 94 32
22Q LOSS WILD-TYPE 234 32

Figure S166.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00316 (Fisher's exact test), Q value = 0.062

Table S167.  Gene #79: '22q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 382 62
22Q LOSS MUTATED 134 10
22Q LOSS WILD-TYPE 248 52

Figure S167.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000273 (Wilcoxon-test), Q value = 0.015

Table S168.  Gene #79: '22q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
22Q LOSS MUTATED 136 2.9 (5.0)
22Q LOSS WILD-TYPE 288 1.7 (4.1)

Figure S168.  Get High-res Image Gene #79: '22q loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00138 (Fisher's exact test), Q value = 0.035

Table S169.  Gene #80: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
XP LOSS MUTATED 25 17 21
XP LOSS WILD-TYPE 237 88 61

Figure S169.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xp loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0334 (Fisher's exact test), Q value = 0.22

Table S170.  Gene #80: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
XP LOSS MUTATED 42 15
XP LOSS WILD-TYPE 286 49

Figure S170.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'xp loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000228 (Wilcoxon-test), Q value = 0.013

Table S171.  Gene #80: 'xp loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
XP LOSS MUTATED 59 3.3 (4.5)
XP LOSS WILD-TYPE 365 1.9 (4.4)

Figure S171.  Get High-res Image Gene #80: 'xp loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'xq loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.024 (Fisher's exact test), Q value = 0.18

Table S172.  Gene #81: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 262 105 82
XQ LOSS MUTATED 21 14 15
XQ LOSS WILD-TYPE 241 91 67

Figure S172.  Get High-res Image Gene #81: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xq loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00997 (Fisher's exact test), Q value = 0.11

Table S173.  Gene #81: 'xq loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 328 64
XQ LOSS MUTATED 32 14
XQ LOSS WILD-TYPE 296 50

Figure S173.  Get High-res Image Gene #81: 'xq loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'xq loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00851 (Wilcoxon-test), Q value = 0.11

Table S174.  Gene #81: 'xq loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 424 2.1 (4.4)
XQ LOSS MUTATED 45 3.0 (4.5)
XQ LOSS WILD-TYPE 379 2.0 (4.4)

Figure S174.  Get High-res Image Gene #81: 'xq loss' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/22508740/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/COAD-TP/22506513/COAD-TP.merged_data.txt

  • Number of patients = 449

  • Number of significantly arm-level cnvs = 81

  • Number of selected clinical features = 13

  • Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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