Correlation between copy number variation genes (focal) and selected clinical features
Colon Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1MG7MDZ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Colon Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1MG7MDZ
Overview
Introduction

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

Summary

Testing the association between copy number variation 68 arm-level results and 11 clinical features across 413 patients, 34 significant findings detected with Q value < 0.25.

  • Amp Peak 11(13q12.13) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 12(13q22.1) cnv correlated to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.

  • Amp Peak 13(16p11.2) cnv correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.

  • Amp Peak 14(16q12.1) cnv correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.

  • Amp Peak 22(20q11.21) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 23(20q12) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 24(20q13.32) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 1(1p36.11) cnv correlated to 'PATHOLOGICSPREAD(M)'.

  • Del Peak 9(4p16.2) cnv correlated to 'Time to Death',  'PATHOLOGY.N', and 'PATHOLOGICSPREAD(M)'.

  • Del Peak 13(5q21.3) cnv correlated to 'PATHOLOGY.N'.

  • Del Peak 18(8p23.3) cnv correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.

  • Del Peak 19(8p22) cnv correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.

  • Del Peak 21(8p11.21) cnv correlated to 'PATHOLOGY.N'.

  • Del Peak 28(13q14.13) cnv correlated to 'PATHOLOGICSPREAD(M)'.

  • Del Peak 35(17p12) cnv correlated to 'HISTOLOGICAL.TYPE',  'PATHOLOGY.N',  'TUMOR.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • Del Peak 37(18p11.31) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 38(18q12.2) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 39(18q21.2) cnv correlated to 'HISTOLOGICAL.TYPE',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • Del Peak 40(18q22.1) cnv correlated to 'HISTOLOGICAL.TYPE',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • Del Peak 41(19p13.3) cnv correlated to 'PATHOLOGY.N'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 68 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 34 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test t-test
Del Peak 35(17p12) 0 (0%) 184 0.334
(1.00) 		0.0108
(1.00) 		0.43
(1.00) 		3.38e-06
(0.0025) 		0.869
(1.00) 		2.64e-05
(0.0193) 		0.0165
(1.00) 		1.19e-06
(0.000883) 		0.257
(1.00) 		0.209
(1.00) 		6.46e-05
(0.047)
Del Peak 9(4p16 2) 0 (0%) 292 0.00024
(0.173) 		0.609
(1.00) 		0.59
(1.00) 		0.036
(1.00) 		0.67
(1.00) 		0.000256
(0.184) 		0.000266
(0.191) 		0.000587
(0.414) 		0.0247
(1.00) 		0.0291
(1.00) 		0.0076
(1.00)
Del Peak 39(18q21 2) 0 (0%) 153 0.4
(1.00) 		0.0992
(1.00) 		0.127
(1.00) 		3.87e-09
(2.88e-06) 		0.805
(1.00) 		0.000112
(0.081) 		0.00624
(1.00) 		9.14e-06
(0.00672) 		0.299
(1.00) 		0.155
(1.00) 		0.0205
(1.00)
Del Peak 40(18q22 1) 0 (0%) 153 0.263
(1.00) 		0.176
(1.00) 		0.127
(1.00) 		4.48e-10
(3.34e-07) 		0.805
(1.00) 		0.000112
(0.081) 		0.00624
(1.00) 		2.02e-05
(0.0148) 		0.299
(1.00) 		0.269
(1.00) 		0.0265
(1.00)
Amp Peak 12(13q22 1) 0 (0%) 159 0.0716
(1.00) 		0.565
(1.00) 		0.363
(1.00) 		8.13e-06
(0.00599) 		1
(1.00) 		0.00143
(0.988) 		0.00698
(1.00) 		0.000315
(0.226) 		0.288
(1.00) 		0.077
(1.00) 		0.0816
(1.00)
Amp Peak 13(16p11 2) 0 (0%) 297 0.426
(1.00) 		0.0688
(1.00) 		0.584
(1.00) 		0.00867
(1.00) 		0.48
(1.00) 		0.000142
(0.102) 		0.323
(1.00) 		0.000162
(0.117) 		1
(1.00) 		0.867
(1.00) 		0.00552
(1.00)
Amp Peak 14(16q12 1) 0 (0%) 311 0.356
(1.00) 		0.0166
(1.00) 		0.493
(1.00) 		0.0112
(1.00) 		0.947
(1.00) 		0.000185
(0.133) 		0.18
(1.00) 		3e-05
(0.022) 		0.574
(1.00) 		0.812
(1.00) 		0.0162
(1.00)
Del Peak 18(8p23 3) 0 (0%) 242 0.566
(1.00) 		0.251
(1.00) 		0.193
(1.00) 		0.0746
(1.00) 		0.165
(1.00) 		0.000318
(0.227) 		0.0225
(1.00) 		9.26e-05
(0.0673) 		0.572
(1.00) 		0.0397
(1.00) 		0.00532
(1.00)
Del Peak 19(8p22) 0 (0%) 228 0.433
(1.00) 		0.104
(1.00) 		0.321
(1.00) 		0.0185
(1.00) 		0.222
(1.00) 		7.69e-06
(0.00567) 		0.00136
(0.946) 		2.17e-07
(0.000161) 		0.589
(1.00) 		0.0225
(1.00) 		0.00105
(0.732)
Amp Peak 11(13q12 13) 0 (0%) 163 0.29
(1.00) 		0.522
(1.00) 		0.92
(1.00) 		8.87e-07
(0.000659) 		0.966
(1.00) 		0.00311
(1.00) 		0.00471
(1.00) 		0.000464
(0.33) 		0.282
(1.00) 		0.0373
(1.00) 		0.0534
(1.00)
Amp Peak 22(20q11 21) 0 (0%) 117 0.433
(1.00) 		0.474
(1.00) 		0.382
(1.00) 		7.66e-06
(0.00566) 		0.542
(1.00) 		0.0243
(1.00) 		0.0102
(1.00) 		0.000866
(0.61) 		0.562
(1.00) 		0.132
(1.00) 		0.0736
(1.00)
Amp Peak 23(20q12) 0 (0%) 116 0.365
(1.00) 		0.51
(1.00) 		0.324
(1.00) 		1.38e-06
(0.00102) 		0.678
(1.00) 		0.0293
(1.00) 		0.00474
(1.00) 		0.000579
(0.41) 		0.563
(1.00) 		0.134
(1.00) 		0.0994
(1.00)
Amp Peak 24(20q13 32) 0 (0%) 113 0.371
(1.00) 		0.537
(1.00) 		0.377
(1.00) 		4.8e-06
(0.00355) 		0.631
(1.00) 		0.0182
(1.00) 		0.00667
(1.00) 		0.000567
(0.402) 		0.565
(1.00) 		0.138
(1.00) 		0.0271
(1.00)
Del Peak 1(1p36 11) 0 (0%) 263 0.0209
(1.00) 		0.144
(1.00) 		0.54
(1.00) 		0.00362
(1.00) 		0.653
(1.00) 		0.00498
(1.00) 		0.000122
(0.0881) 		0.000885
(0.622) 		1
(1.00) 		0.0322
(1.00) 		0.0061
(1.00)
Del Peak 13(5q21 3) 0 (0%) 296 0.0728
(1.00) 		0.0679
(1.00) 		0.743
(1.00) 		0.196
(1.00) 		0.976
(1.00) 		5.3e-05
(0.0387) 		0.0201
(1.00) 		0.000579
(0.41) 		0.0223
(1.00) 		0.0902
(1.00) 		0.00516
(1.00)
Del Peak 21(8p11 21) 0 (0%) 370 0.826
(1.00) 		0.377
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.155
(1.00) 		0.000316
(0.226) 		0.00793
(1.00) 		0.00102
(0.714) 		0.282
(1.00) 		0.121
(1.00) 		0.0181
(1.00)
Del Peak 28(13q14 13) 0 (0%) 395 0.312
(1.00) 		0.279
(1.00) 		1
(1.00) 		1
(1.00) 		0.719
(1.00) 		0.0629
(1.00) 		4.33e-05
(0.0316) 		0.835
(1.00) 		1
(1.00) 		0.726
(1.00) 		0.223
(1.00)
Del Peak 37(18p11 31) 0 (0%) 193 0.869
(1.00) 		0.0199
(1.00) 		1
(1.00) 		8.39e-11
(6.28e-08) 		0.819
(1.00) 		0.0479
(1.00) 		0.00385
(1.00) 		0.00181
(1.00) 		0.251
(1.00) 		0.0655
(1.00) 		0.375
(1.00)
Del Peak 38(18q12 2) 0 (0%) 166 0.983
(1.00) 		0.0542
(1.00) 		0.421
(1.00) 		3.02e-10
(2.25e-07) 		0.838
(1.00) 		0.002
(1.00) 		0.0125
(1.00) 		0.000376
(0.268) 		0.277
(1.00) 		0.149
(1.00) 		0.087
(1.00)
Del Peak 41(19p13 3) 0 (0%) 356 0.367
(1.00) 		0.148
(1.00) 		0.67
(1.00) 		0.202
(1.00) 		0.956
(1.00) 		5.85e-05
(0.0426) 		0.0321
(1.00) 		0.00168
(1.00) 		0.36
(1.00) 		0.0219
(1.00) 		0.00169
(1.00)
Amp Peak 1(2q33 1) 0 (0%) 334 0.0421
(1.00) 		0.358
(1.00) 		0.259
(1.00) 		0.267
(1.00) 		0.834
(1.00) 		0.0212
(1.00) 		0.639
(1.00) 		0.0501
(1.00) 		0.472
(1.00) 		0.119
(1.00) 		0.0758
(1.00)
Amp Peak 2(5p13 2) 0 (0%) 332 0.344
(1.00) 		0.234
(1.00) 		0.322
(1.00) 		0.856
(1.00) 		0.521
(1.00) 		0.034
(1.00) 		0.729
(1.00) 		0.771
(1.00) 		1
(1.00) 		0.209
(1.00) 		0.0458
(1.00)
Amp Peak 3(5q22 3) 0 (0%) 373 0.975
(1.00) 		0.768
(1.00) 		0.74
(1.00) 		0.332
(1.00) 		0.781
(1.00) 		0.201
(1.00) 		0.00941
(1.00) 		0.0736
(1.00) 		0.264
(1.00) 		0.0908
(1.00) 		0.266
(1.00)
Amp Peak 4(6p21 1) 0 (0%) 324 0.855
(1.00) 		0.829
(1.00) 		0.283
(1.00) 		0.0505
(1.00) 		0.568
(1.00) 		0.00138
(0.957) 		0.609
(1.00) 		0.0106
(1.00) 		0.00974
(1.00) 		0.254
(1.00) 		0.013
(1.00)
Amp Peak 5(8p11 23) 0 (0%) 269 0.875
(1.00) 		0.293
(1.00) 		0.757
(1.00) 		0.168
(1.00) 		0.791
(1.00) 		0.721
(1.00) 		0.569
(1.00) 		0.928
(1.00) 		0.279
(1.00) 		0.434
(1.00) 		0.856
(1.00)
Amp Peak 6(8p11 21) 0 (0%) 240 0.419
(1.00) 		0.449
(1.00) 		0.272
(1.00) 		0.184
(1.00) 		0.765
(1.00) 		0.556
(1.00) 		0.466
(1.00) 		0.958
(1.00) 		0.574
(1.00) 		0.501
(1.00) 		0.867
(1.00)
Amp Peak 7(8q12 1) 0 (0%) 198 0.858
(1.00) 		0.113
(1.00) 		0.844
(1.00) 		0.0189
(1.00) 		0.417
(1.00) 		0.362
(1.00) 		0.158
(1.00) 		0.394
(1.00) 		0.249
(1.00) 		0.341
(1.00) 		0.0598
(1.00)
Amp Peak 8(8q24 21) 0 (0%) 174 0.637
(1.00) 		0.074
(1.00) 		0.485
(1.00) 		0.0753
(1.00) 		0.2
(1.00) 		0.282
(1.00) 		0.0847
(1.00) 		0.25
(1.00) 		0.267
(1.00) 		0.375
(1.00) 		0.0494
(1.00)
Amp Peak 9(11p15 5) 0 (0%) 327 0.603
(1.00) 		0.0407
(1.00) 		0.544
(1.00) 		0.00194
(1.00) 		0.151
(1.00) 		0.276
(1.00) 		0.254
(1.00) 		0.154
(1.00) 		0.111
(1.00) 		0.212
(1.00) 		0.265
(1.00)
Amp Peak 10(12p13 33) 0 (0%) 309 0.2
(1.00) 		0.139
(1.00) 		0.734
(1.00) 		0.501
(1.00) 		0.16
(1.00) 		0.144
(1.00) 		0.2
(1.00) 		0.112
(1.00) 		0.575
(1.00) 		0.519
(1.00) 		0.829
(1.00)
Amp Peak 15(17q12) 0 (0%) 312 0.479
(1.00) 		0.45
(1.00) 		0.252
(1.00) 		0.313
(1.00) 		0.25
(1.00) 		0.113
(1.00) 		0.0126
(1.00) 		0.0172
(1.00) 		0.57
(1.00) 		0.112
(1.00) 		0.144
(1.00)
Amp Peak 16(17q24 1) 0 (0%) 321 0.076
(1.00) 		0.414
(1.00) 		0.638
(1.00) 		0.112
(1.00) 		0.409
(1.00) 		0.341
(1.00) 		0.0351
(1.00) 		0.21
(1.00) 		0.531
(1.00) 		0.205
(1.00) 		0.961
(1.00)
Amp Peak 17(19p13 2) 0 (0%) 348 0.63
(1.00) 		0.618
(1.00) 		0.0575
(1.00) 		0.228
(1.00) 		0.655
(1.00) 		0.0194
(1.00) 		0.00672
(1.00) 		0.231
(1.00) 		0.403
(1.00) 		0.137
(1.00) 		0.354
(1.00)
Amp Peak 18(19q13 11) 0 (0%) 330 0.201
(1.00) 		0.68
(1.00) 		0.0648
(1.00) 		0.364
(1.00) 		0.942
(1.00) 		0.129
(1.00) 		0.0224
(1.00) 		0.486
(1.00) 		0.491
(1.00) 		0.686
(1.00) 		0.966
(1.00)
Amp Peak 19(20p12 3) 0 (0%) 229 0.0533
(1.00) 		0.491
(1.00) 		0.197
(1.00) 		0.0554
(1.00) 		0.962
(1.00) 		0.0795
(1.00) 		0.00371
(1.00) 		0.00697
(1.00) 		0.0876
(1.00) 		0.0245
(1.00) 		0.0123
(1.00)
Amp Peak 20(20p11 23) 0 (0%) 208 0.234
(1.00) 		0.974
(1.00) 		0.2
(1.00) 		0.0127
(1.00) 		0.947
(1.00) 		0.0614
(1.00) 		0.00206
(1.00) 		0.00876
(1.00) 		0.121
(1.00) 		0.0242
(1.00) 		0.124
(1.00)
Amp Peak 21(20p11 21) 0 (0%) 183 0.453
(1.00) 		0.466
(1.00) 		0.165
(1.00) 		0.00494
(1.00) 		0.897
(1.00) 		0.272
(1.00) 		0.00305
(1.00) 		0.0131
(1.00) 		0.258
(1.00) 		0.0488
(1.00) 		0.323
(1.00)
Del Peak 2(1p33) 0 (0%) 306 0.00122
(0.848) 		0.89
(1.00) 		0.91
(1.00) 		0.132
(1.00) 		0.505
(1.00) 		0.00466
(1.00) 		0.00786
(1.00) 		0.0144
(1.00) 		0.572
(1.00) 		0.0993
(1.00) 		0.0145
(1.00)
Del Peak 3(1p13 1) 0 (0%) 310 0.0503
(1.00) 		0.891
(1.00) 		0.496
(1.00) 		0.133
(1.00) 		0.541
(1.00) 		0.00105
(0.733) 		0.000797
(0.562) 		0.00869
(1.00) 		1
(1.00) 		0.0566
(1.00) 		0.00935
(1.00)
Del Peak 4(1q43) 0 (0%) 369 0.488
(1.00) 		0.525
(1.00) 		0.875
(1.00) 		0.818
(1.00) 		0.3
(1.00) 		0.179
(1.00) 		0.077
(1.00) 		0.158
(1.00) 		0.287
(1.00) 		0.0922
(1.00) 		0.291
(1.00)
Del Peak 5(2q37 2) 0 (0%) 392 0.368
(1.00) 		0.447
(1.00) 		0.374
(1.00) 		0.748
(1.00) 		0.447
(1.00) 		0.825
(1.00) 		0.361
(1.00) 		0.454
(1.00) 		1
(1.00) 		1
(1.00) 		0.168
(1.00)
Del Peak 6(3p26 1) 0 (0%) 353 0.000411
(0.293) 		0.346
(1.00) 		1
(1.00) 		0.146
(1.00) 		0.0583
(1.00) 		0.0186
(1.00) 		0.000457
(0.325) 		0.000553
(0.393) 		1
(1.00) 		0.0726
(1.00) 		0.177
(1.00)
Del Peak 7(3p14 2) 0 (0%) 338 0.426
(1.00) 		0.608
(1.00) 		0.371
(1.00) 		0.186
(1.00) 		0.189
(1.00) 		0.0486
(1.00) 		0.0569
(1.00) 		0.0529
(1.00) 		1
(1.00) 		0.123
(1.00) 		0.0322
(1.00)
Del Peak 8(3q26 31) 0 (0%) 374 0.452
(1.00) 		0.85
(1.00) 		1
(1.00) 		0.14
(1.00) 		0.0989
(1.00) 		0.595
(1.00) 		0.619
(1.00) 		0.168
(1.00) 		1
(1.00) 		0.599
(1.00) 		0.374
(1.00)
Del Peak 10(4q22 1) 0 (0%) 287 0.009
(1.00) 		0.967
(1.00) 		0.593
(1.00) 		0.0174
(1.00) 		0.341
(1.00) 		0.00186
(1.00) 		0.118
(1.00) 		0.0169
(1.00) 		0.0279
(1.00) 		0.436
(1.00) 		0.0153
(1.00)
Del Peak 11(4q35 1) 0 (0%) 276 0.0437
(1.00) 		0.255
(1.00) 		0.249
(1.00) 		0.0871
(1.00) 		0.72
(1.00) 		0.00586
(1.00) 		0.221
(1.00) 		0.0424
(1.00) 		0.036
(1.00) 		0.14
(1.00) 		0.0635
(1.00)
Del Peak 12(5q11 2) 0 (0%) 322 0.0477
(1.00) 		0.0453
(1.00) 		0.408
(1.00) 		0.112
(1.00) 		0.899
(1.00) 		0.00319
(1.00) 		0.0574
(1.00) 		0.00895
(1.00) 		0.124
(1.00) 		0.269
(1.00) 		0.0149
(1.00)
Del Peak 14(5q23 1) 0 (0%) 306 0.129
(1.00) 		0.285
(1.00) 		0.311
(1.00) 		0.0983
(1.00) 		0.946
(1.00) 		0.00593
(1.00) 		0.0116
(1.00) 		0.0366
(1.00) 		0.017
(1.00) 		0.109
(1.00) 		0.0287
(1.00)
Del Peak 15(6p25 3) 0 (0%) 359 0.704
(1.00) 		0.0948
(1.00) 		0.0794
(1.00) 		0.516
(1.00) 		0.126
(1.00) 		0.932
(1.00) 		0.18
(1.00) 		0.825
(1.00) 		1
(1.00) 		0.297
(1.00) 		0.738
(1.00)
Del Peak 16(6q26) 0 (0%) 353 0.0205
(1.00) 		0.928
(1.00) 		0.782
(1.00) 		1
(1.00) 		0.194
(1.00) 		0.0248
(1.00) 		0.0212
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.0169
(1.00) 		0.0144
(1.00)
Del Peak 17(7q31 1) 0 (0%) 402 0.978
(1.00) 		0.589
(1.00) 		0.36
(1.00) 		1
(1.00) 		0.571
(1.00) 		1
(1.00) 		0.498
(1.00) 		0.493
(1.00) 		1
(1.00) 		1
(1.00) 		0.666
(1.00)
Del Peak 20(8p11 22) 0 (0%) 333 0.412
(1.00) 		0.236
(1.00) 		0.803
(1.00) 		0.461
(1.00) 		0.342
(1.00) 		0.000914
(0.642) 		0.0887
(1.00) 		0.00266
(1.00) 		0.0973
(1.00) 		0.248
(1.00) 		0.0333
(1.00)
Del Peak 22(9p21 3) 0 (0%) 357 0.0248
(1.00) 		0.0603
(1.00) 		0.251
(1.00) 		0.202
(1.00) 		0.292
(1.00) 		0.144
(1.00) 		0.106
(1.00) 		0.399
(1.00) 		1
(1.00) 		0.272
(1.00) 		0.309
(1.00)
Del Peak 23(10p15 3) 0 (0%) 345 0.847
(1.00) 		0.434
(1.00) 		0.791
(1.00) 		0.557
(1.00) 		0.856
(1.00) 		0.00164
(1.00) 		0.00231
(1.00) 		0.0011
(0.765) 		0.0717
(1.00) 		0.547
(1.00) 		0.0712
(1.00)
Del Peak 24(10q21 1) 0 (0%) 331 0.959
(1.00) 		0.0528
(1.00) 		0.388
(1.00) 		0.0995
(1.00) 		0.952
(1.00) 		0.00851
(1.00) 		0.0976
(1.00) 		0.0196
(1.00) 		0.102
(1.00) 		0.0115
(1.00) 		0.0801
(1.00)
Del Peak 25(10q23 31) 0 (0%) 319 0.834
(1.00) 		0.0124
(1.00) 		0.483
(1.00) 		0.164
(1.00) 		0.503
(1.00) 		0.00523
(1.00) 		0.00814
(1.00) 		0.0221
(1.00) 		0.131
(1.00) 		0.0496
(1.00) 		0.0907
(1.00)
Del Peak 26(10q25 2) 0 (0%) 320 0.313
(1.00) 		0.164
(1.00) 		0.907
(1.00) 		0.164
(1.00) 		0.227
(1.00) 		0.00365
(1.00) 		0.0681
(1.00) 		0.0169
(1.00) 		0.129
(1.00) 		0.0132
(1.00) 		0.0781
(1.00)
Del Peak 27(12p13 2) 0 (0%) 369 0.384
(1.00) 		0.633
(1.00) 		0.338
(1.00) 		0.00188
(1.00) 		0.897
(1.00) 		0.0822
(1.00) 		0.166
(1.00) 		0.0971
(1.00) 		1
(1.00) 		0.619
(1.00) 		0.697
(1.00)
Del Peak 29(14q32 11) 0 (0%) 280 0.353
(1.00) 		0.506
(1.00) 		0.674
(1.00) 		0.000917
(0.643) 		0.631
(1.00) 		0.0613
(1.00) 		0.0367
(1.00) 		0.00434
(1.00) 		0.554
(1.00) 		0.326
(1.00) 		0.136
(1.00)
Del Peak 30(15q11 2) 0 (0%) 253 0.93
(1.00) 		0.852
(1.00) 		1
(1.00) 		0.0238
(1.00) 		0.912
(1.00) 		0.0115
(1.00) 		0.0635
(1.00) 		0.00321
(1.00) 		0.0575
(1.00) 		0.321
(1.00) 		0.252
(1.00)
Del Peak 31(15q21 1) 0 (0%) 262 0.0937
(1.00) 		0.658
(1.00) 		0.919
(1.00) 		0.0488
(1.00) 		0.965
(1.00) 		0.0824
(1.00) 		0.0887
(1.00) 		0.0559
(1.00) 		0.0483
(1.00) 		0.547
(1.00) 		0.467
(1.00)
Del Peak 32(15q22 33) 0 (0%) 268 0.255
(1.00) 		0.426
(1.00) 		0.918
(1.00) 		0.00592
(1.00) 		0.58
(1.00) 		0.0403
(1.00) 		0.0478
(1.00) 		0.0218
(1.00) 		0.0427
(1.00) 		0.511
(1.00) 		0.33
(1.00)
Del Peak 33(16p13 3) 0 (0%) 368 0.00179
(1.00) 		0.426
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.0362
(1.00) 		0.0647
(1.00) 		0.357
(1.00) 		0.163
(1.00) 		1
(1.00) 		0.724
(1.00) 		0.109
(1.00)
Del Peak 34(16q23 1) 0 (0%) 364 0.00129
(0.894) 		0.288
(1.00) 		0.129
(1.00) 		0.261
(1.00) 		0.631
(1.00) 		0.384
(1.00) 		0.979
(1.00) 		0.896
(1.00) 		1
(1.00) 		0.872
(1.00) 		0.26
(1.00)
Del Peak 36(17q24 3) 0 (0%) 354 0.729
(1.00) 		0.51
(1.00) 		0.328
(1.00) 		1
(1.00) 		0.687
(1.00) 		0.00836
(1.00) 		0.253
(1.00) 		0.0329
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.0379
(1.00)
Del Peak 42(20p12 1) 0 (0%) 334 0.803
(1.00) 		0.439
(1.00) 		0.618
(1.00) 		0.137
(1.00) 		0.695
(1.00) 		0.553
(1.00) 		0.983
(1.00) 		0.419
(1.00) 		1
(1.00) 		0.686
(1.00) 		0.531
(1.00)
Del Peak 43(21q11 2) 0 (0%) 288 0.468
(1.00) 		0.722
(1.00) 		1
(1.00) 		0.0101
(1.00) 		0.267
(1.00) 		0.0417
(1.00) 		0.344
(1.00) 		0.187
(1.00) 		0.219
(1.00) 		0.395
(1.00) 		0.0108
(1.00)
Del Peak 44(22q13 32) 0 (0%) 275 0.208
(1.00) 		0.701
(1.00) 		0.603
(1.00) 		0.00499
(1.00) 		0.732
(1.00) 		0.00257
(1.00) 		0.0348
(1.00) 		0.014
(1.00) 		1
(1.00) 		0.239
(1.00) 		0.00975
(1.00)
'Amp Peak 11(13q12.13)' versus 'HISTOLOGICAL.TYPE'

P value = 8.87e-07 (Fisher's exact test), Q value = 0.00066

Table S1.  Gene #11: 'Amp Peak 11(13q12.13)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 356 54
AMP PEAK 11(13Q12.13) CNV 233 16
AMP PEAK 11(13Q12.13) WILD-TYPE 123 38

Figure S1.  Get High-res Image Gene #11: 'Amp Peak 11(13q12.13)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 12(13q22.1)' versus 'HISTOLOGICAL.TYPE'

P value = 8.13e-06 (Fisher's exact test), Q value = 0.006

Table S2.  Gene #12: 'Amp Peak 12(13q22.1)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 356 54
AMP PEAK 12(13Q22.1) CNV 235 18
AMP PEAK 12(13Q22.1) WILD-TYPE 121 36

Figure S2.  Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 12(13q22.1)' versus 'TUMOR.STAGE'

P value = 0.000315 (Fisher's exact test), Q value = 0.23

Table S3.  Gene #12: 'Amp Peak 12(13q22.1)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients I II III IV
ALL 67 157 116 56
AMP PEAK 12(13Q22.1) CNV 40 79 78 45
AMP PEAK 12(13Q22.1) WILD-TYPE 27 78 38 11

Figure S3.  Get High-res Image Gene #12: 'Amp Peak 12(13q22.1)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Amp Peak 13(16p11.2)' versus 'PATHOLOGY.N'

P value = 0.000142 (Fisher's exact test), Q value = 0.1

Table S4.  Gene #13: 'Amp Peak 13(16p11.2)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 245 95 71
AMP PEAK 13(16P11.2) CNV 50 35 30
AMP PEAK 13(16P11.2) WILD-TYPE 195 60 41

Figure S4.  Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Clinical Feature #6: 'PATHOLOGY.N'

'Amp Peak 13(16p11.2)' versus 'TUMOR.STAGE'

P value = 0.000162 (Fisher's exact test), Q value = 0.12

Table S5.  Gene #13: 'Amp Peak 13(16p11.2)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients I II III IV
ALL 67 157 116 56
AMP PEAK 13(16P11.2) CNV 12 30 48 18
AMP PEAK 13(16P11.2) WILD-TYPE 55 127 68 38

Figure S5.  Get High-res Image Gene #13: 'Amp Peak 13(16p11.2)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Amp Peak 14(16q12.1)' versus 'PATHOLOGY.N'

P value = 0.000185 (Fisher's exact test), Q value = 0.13

Table S6.  Gene #14: 'Amp Peak 14(16q12.1)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 245 95 71
AMP PEAK 14(16Q12.1) CNV 43 33 26
AMP PEAK 14(16Q12.1) WILD-TYPE 202 62 45

Figure S6.  Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Clinical Feature #6: 'PATHOLOGY.N'

'Amp Peak 14(16q12.1)' versus 'TUMOR.STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.022

Table S7.  Gene #14: 'Amp Peak 14(16q12.1)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients I II III IV
ALL 67 157 116 56
AMP PEAK 14(16Q12.1) CNV 12 23 46 14
AMP PEAK 14(16Q12.1) WILD-TYPE 55 134 70 42

Figure S7.  Get High-res Image Gene #14: 'Amp Peak 14(16q12.1)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Amp Peak 22(20q11.21)' versus 'HISTOLOGICAL.TYPE'

P value = 7.66e-06 (Fisher's exact test), Q value = 0.0057

Table S8.  Gene #22: 'Amp Peak 22(20q11.21)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 356 54
AMP PEAK 22(20Q11.21) CNV 269 24
AMP PEAK 22(20Q11.21) WILD-TYPE 87 30

Figure S8.  Get High-res Image Gene #22: 'Amp Peak 22(20q11.21)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 23(20q12)' versus 'HISTOLOGICAL.TYPE'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.001

Table S9.  Gene #23: 'Amp Peak 23(20q12)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 356 54
AMP PEAK 23(20Q12) CNV 271 23
AMP PEAK 23(20Q12) WILD-TYPE 85 31

Figure S9.  Get High-res Image Gene #23: 'Amp Peak 23(20q12)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 24(20q13.32)' versus 'HISTOLOGICAL.TYPE'

P value = 4.8e-06 (Fisher's exact test), Q value = 0.0035

Table S10.  Gene #24: 'Amp Peak 24(20q13.32)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 356 54
AMP PEAK 24(20Q13.32) CNV 273 24
AMP PEAK 24(20Q13.32) WILD-TYPE 83 30

Figure S10.  Get High-res Image Gene #24: 'Amp Peak 24(20q13.32)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 1(1p36.11)' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000122 (Chi-square test), Q value = 0.088

Table S11.  Gene #25: 'Del Peak 1(1p36.11)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients M0 M1 M1A M1B MX
ALL 312 49 7 1 36
DEL PEAK 1(1P36.11) CNV 101 33 2 0 13
DEL PEAK 1(1P36.11) WILD-TYPE 211 16 5 1 23

Figure S11.  Get High-res Image Gene #25: 'Del Peak 1(1p36.11)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 9(4p16.2)' versus 'Time to Death'

P value = 0.00024 (logrank test), Q value = 0.17

Table S12.  Gene #33: 'Del Peak 9(4p16.2)' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 319 49 0.1 - 135.5 (7.7)
DEL PEAK 9(4P16.2) CNV 89 20 0.2 - 87.8 (7.6)
DEL PEAK 9(4P16.2) WILD-TYPE 230 29 0.1 - 135.5 (8.0)

Figure S12.  Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 9(4p16.2)' versus 'PATHOLOGY.N'

P value = 0.000256 (Fisher's exact test), Q value = 0.18

Table S13.  Gene #33: 'Del Peak 9(4p16.2)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 245 95 71
DEL PEAK 9(4P16.2) CNV 54 34 32
DEL PEAK 9(4P16.2) WILD-TYPE 191 61 39

Figure S13.  Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 9(4p16.2)' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000266 (Chi-square test), Q value = 0.19

Table S14.  Gene #33: 'Del Peak 9(4p16.2)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients M0 M1 M1A M1B MX
ALL 312 49 7 1 36
DEL PEAK 9(4P16.2) CNV 75 27 3 0 12
DEL PEAK 9(4P16.2) WILD-TYPE 237 22 4 1 24

Figure S14.  Get High-res Image Gene #33: 'Del Peak 9(4p16.2)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 13(5q21.3)' versus 'PATHOLOGY.N'

P value = 5.3e-05 (Fisher's exact test), Q value = 0.039

Table S15.  Gene #37: 'Del Peak 13(5q21.3)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 245 95 71
DEL PEAK 13(5Q21.3) CNV 50 34 32
DEL PEAK 13(5Q21.3) WILD-TYPE 195 61 39

Figure S15.  Get High-res Image Gene #37: 'Del Peak 13(5q21.3)' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 18(8p23.3)' versus 'PATHOLOGY.N'

P value = 0.000318 (Fisher's exact test), Q value = 0.23

Table S16.  Gene #42: 'Del Peak 18(8p23.3)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 245 95 71
DEL PEAK 18(8P23.3) CNV 82 46 41
DEL PEAK 18(8P23.3) WILD-TYPE 163 49 30

Figure S16.  Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 18(8p23.3)' versus 'TUMOR.STAGE'

P value = 9.26e-05 (Fisher's exact test), Q value = 0.067

Table S17.  Gene #42: 'Del Peak 18(8p23.3)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients I II III IV
ALL 67 157 116 56
DEL PEAK 18(8P23.3) CNV 24 48 59 34
DEL PEAK 18(8P23.3) WILD-TYPE 43 109 57 22

Figure S17.  Get High-res Image Gene #42: 'Del Peak 18(8p23.3)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 19(8p22)' versus 'PATHOLOGY.N'

P value = 7.69e-06 (Fisher's exact test), Q value = 0.0057

Table S18.  Gene #43: 'Del Peak 19(8p22)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 245 95 71
DEL PEAK 19(8P22) CNV 87 49 47
DEL PEAK 19(8P22) WILD-TYPE 158 46 24

Figure S18.  Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 19(8p22)' versus 'TUMOR.STAGE'

P value = 2.17e-07 (Fisher's exact test), Q value = 0.00016

Table S19.  Gene #43: 'Del Peak 19(8p22)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients I II III IV
ALL 67 157 116 56
DEL PEAK 19(8P22) CNV 24 50 66 39
DEL PEAK 19(8P22) WILD-TYPE 43 107 50 17

Figure S19.  Get High-res Image Gene #43: 'Del Peak 19(8p22)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 21(8p11.21)' versus 'PATHOLOGY.N'

P value = 0.000316 (Fisher's exact test), Q value = 0.23

Table S20.  Gene #45: 'Del Peak 21(8p11.21)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 245 95 71
DEL PEAK 21(8P11.21) CNV 14 14 15
DEL PEAK 21(8P11.21) WILD-TYPE 231 81 56

Figure S20.  Get High-res Image Gene #45: 'Del Peak 21(8p11.21)' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 28(13q14.13)' versus 'PATHOLOGICSPREAD(M)'

P value = 4.33e-05 (Chi-square test), Q value = 0.032

Table S21.  Gene #52: 'Del Peak 28(13q14.13)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients M0 M1 M1A M1B MX
ALL 312 49 7 1 36
DEL PEAK 28(13Q14.13) CNV 12 1 0 1 2
DEL PEAK 28(13Q14.13) WILD-TYPE 300 48 7 0 34

Figure S21.  Get High-res Image Gene #52: 'Del Peak 28(13q14.13)' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 35(17p12)' versus 'HISTOLOGICAL.TYPE'

P value = 3.38e-06 (Fisher's exact test), Q value = 0.0025

Table S22.  Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 356 54
DEL PEAK 35(17P12) CNV 213 14
DEL PEAK 35(17P12) WILD-TYPE 143 40

Figure S22.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 35(17p12)' versus 'PATHOLOGY.N'

P value = 2.64e-05 (Fisher's exact test), Q value = 0.019

Table S23.  Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 245 95 71
DEL PEAK 35(17P12) CNV 113 63 51
DEL PEAK 35(17P12) WILD-TYPE 132 32 20

Figure S23.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 35(17p12)' versus 'TUMOR.STAGE'

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00088

Table S24.  Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients I II III IV
ALL 67 157 116 56
DEL PEAK 35(17P12) CNV 34 64 80 41
DEL PEAK 35(17P12) WILD-TYPE 33 93 36 15

Figure S24.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 35(17p12)' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.46e-05 (t-test), Q value = 0.047

Table S25.  Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 389 2.0 (4.5)
DEL PEAK 35(17P12) CNV 216 2.8 (5.5)
DEL PEAK 35(17P12) WILD-TYPE 173 1.1 (2.4)

Figure S25.  Get High-res Image Gene #59: 'Del Peak 35(17p12)' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 37(18p11.31)' versus 'HISTOLOGICAL.TYPE'

P value = 8.39e-11 (Fisher's exact test), Q value = 6.3e-08

Table S26.  Gene #61: 'Del Peak 37(18p11.31)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 356 54
DEL PEAK 37(18P11.31) CNV 211 7
DEL PEAK 37(18P11.31) WILD-TYPE 145 47

Figure S26.  Get High-res Image Gene #61: 'Del Peak 37(18p11.31)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 38(18q12.2)' versus 'HISTOLOGICAL.TYPE'

P value = 3.02e-10 (Fisher's exact test), Q value = 2.3e-07

Table S27.  Gene #62: 'Del Peak 38(18q12.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 356 54
DEL PEAK 38(18Q12.2) CNV 235 11
DEL PEAK 38(18Q12.2) WILD-TYPE 121 43

Figure S27.  Get High-res Image Gene #62: 'Del Peak 38(18q12.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 39(18q21.2)' versus 'HISTOLOGICAL.TYPE'

P value = 3.87e-09 (Fisher's exact test), Q value = 2.9e-06

Table S28.  Gene #63: 'Del Peak 39(18q21.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 356 54
DEL PEAK 39(18Q21.2) CNV 245 14
DEL PEAK 39(18Q21.2) WILD-TYPE 111 40

Figure S28.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 39(18q21.2)' versus 'PATHOLOGY.N'

P value = 0.000112 (Fisher's exact test), Q value = 0.081

Table S29.  Gene #63: 'Del Peak 39(18q21.2)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 245 95 71
DEL PEAK 39(18Q21.2) CNV 134 68 56
DEL PEAK 39(18Q21.2) WILD-TYPE 111 27 15

Figure S29.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 39(18q21.2)' versus 'TUMOR.STAGE'

P value = 9.14e-06 (Fisher's exact test), Q value = 0.0067

Table S30.  Gene #63: 'Del Peak 39(18q21.2)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients I II III IV
ALL 67 157 116 56
DEL PEAK 39(18Q21.2) CNV 36 81 83 47
DEL PEAK 39(18Q21.2) WILD-TYPE 31 76 33 9

Figure S30.  Get High-res Image Gene #63: 'Del Peak 39(18q21.2)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 40(18q22.1)' versus 'HISTOLOGICAL.TYPE'

P value = 4.48e-10 (Fisher's exact test), Q value = 3.3e-07

Table S31.  Gene #64: 'Del Peak 40(18q22.1)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
ALL 356 54
DEL PEAK 40(18Q22.1) CNV 246 13
DEL PEAK 40(18Q22.1) WILD-TYPE 110 41

Figure S31.  Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 40(18q22.1)' versus 'PATHOLOGY.N'

P value = 0.000112 (Fisher's exact test), Q value = 0.081

Table S32.  Gene #64: 'Del Peak 40(18q22.1)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 245 95 71
DEL PEAK 40(18Q22.1) CNV 134 68 56
DEL PEAK 40(18Q22.1) WILD-TYPE 111 27 15

Figure S32.  Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 40(18q22.1)' versus 'TUMOR.STAGE'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.015

Table S33.  Gene #64: 'Del Peak 40(18q22.1)' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients I II III IV
ALL 67 157 116 56
DEL PEAK 40(18Q22.1) CNV 36 82 82 47
DEL PEAK 40(18Q22.1) WILD-TYPE 31 75 34 9

Figure S33.  Get High-res Image Gene #64: 'Del Peak 40(18q22.1)' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 41(19p13.3)' versus 'PATHOLOGY.N'

P value = 5.85e-05 (Fisher's exact test), Q value = 0.043

Table S34.  Gene #65: 'Del Peak 41(19p13.3)' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients N0 N1 N2
ALL 245 95 71
DEL PEAK 41(19P13.3) CNV 22 13 22
DEL PEAK 41(19P13.3) WILD-TYPE 223 82 49

Figure S34.  Get High-res Image Gene #65: 'Del Peak 41(19p13.3)' versus Clinical Feature #6: 'PATHOLOGY.N'

Methods & Data
Input

  • Mutation data file = all_lesions.conf_99.cnv.cluster.txt

  • Clinical data file = COAD-TP.clin.merged.picked.txt

  • Number of patients = 413

  • Number of significantly arm-level cnvs = 68

  • Number of selected clinical features = 11

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

Survival analysis

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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] 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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