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

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

Summary

Testing the association between subtypes identified by 68 different clustering approaches and 9 clinical features across 413 patients, 35 significant findings detected with Q value < 0.25.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 1(2q33.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 2(5p13.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 3(5q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 4(6p21.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 5(8p11.23) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 6(8p11.21) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 7(8q12.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 8(8q24.21) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 9(11p15.5) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 10(12p13.33) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 11(13q12.13) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 12(13q22.1) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 13(16p11.2) mutation analysis'. These subtypes correlate to 'PATHOLOGY.N' and 'TUMOR.STAGE'.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 14(16q12.1) mutation analysis'. These subtypes correlate to 'PATHOLOGY.N' and 'TUMOR.STAGE'.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 15(17q12) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 16(17q24.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 17(19p13.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 18(19q13.11) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 19(20p12.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 20(20p11.23) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 21(20p11.21) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 22(20q11.21) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 23(20q12) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 24(20q13.32) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 1(1p36.11) mutation analysis'. These subtypes correlate to 'PATHOLOGICSPREAD(M)'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 2(1p33) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 3(1p13.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 4(1q43) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 5(2q37.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 6(3p26.1) mutation analysis'. These subtypes correlate to 'Time to Death'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 7(3p14.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 8(3q26.31) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 9(4p16.2) mutation analysis'. These subtypes correlate to 'Time to Death',  'PATHOLOGY.N', and 'PATHOLOGICSPREAD(M)'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 10(4q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 11(4q35.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 12(5q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 13(5q21.3) mutation analysis'. These subtypes correlate to 'PATHOLOGY.N'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 14(5q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 15(6p25.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 16(6q26) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 17(7q31.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 18(8p23.3) mutation analysis'. These subtypes correlate to 'PATHOLOGY.N' and 'TUMOR.STAGE'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 19(8p22) mutation analysis'. These subtypes correlate to 'PATHOLOGY.N' and 'TUMOR.STAGE'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 20(8p11.22) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 21(8p11.21) mutation analysis'. These subtypes correlate to 'PATHOLOGY.N'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 22(9p21.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 23(10p15.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 24(10q21.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 25(10q23.31) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 26(10q25.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 27(12p13.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 28(13q14.13) mutation analysis'. These subtypes correlate to 'PATHOLOGICSPREAD(M)'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 29(14q32.11) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 30(15q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 31(15q21.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 32(15q22.33) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 33(16p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 34(16q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 35(17p12) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 36(17q24.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 37(18p11.31) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 38(18q12.2) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 39(18q21.2) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 40(18q22.1) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE',  'PATHOLOGY.N', and 'TUMOR.STAGE'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 41(19p13.3) mutation analysis'. These subtypes correlate to 'PATHOLOGY.N'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 42(20p12.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 43(21q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 44(22q13.32) mutation analysis'. These subtypes do not correlate to any clinical features.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between subtypes identified by 68 different clustering approaches and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 35 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER HISTOLOGICAL
TYPE 		PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		RADIATIONS
RADIATION
REGIMENINDICATION
Statistical Tests 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
Amp Peak 1(2q33 1) 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)
Amp Peak 2(5p13 2) 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)
Amp Peak 3(5q22 3) 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)
Amp Peak 4(6p21 1) 0.855
(1.00) 		0.829
(1.00) 		0.283
(1.00) 		0.0505
(1.00) 		0.568
(1.00) 		0.00138
(0.772) 		0.609
(1.00) 		0.0106
(1.00) 		0.00974
(1.00)
Amp Peak 5(8p11 23) 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)
Amp Peak 6(8p11 21) 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)
Amp Peak 7(8q12 1) 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)
Amp Peak 8(8q24 21) 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)
Amp Peak 9(11p15 5) 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)
Amp Peak 10(12p13 33) 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)
Amp Peak 11(13q12 13) 0.29
(1.00) 		0.522
(1.00) 		0.92
(1.00) 		8.87e-07
(0.000538) 		0.966
(1.00) 		0.00311
(1.00) 		0.00471
(1.00) 		0.000464
(0.267) 		0.282
(1.00)
Amp Peak 12(13q22 1) 0.0716
(1.00) 		0.565
(1.00) 		0.363
(1.00) 		8.13e-06
(0.00488) 		1
(1.00) 		0.00143
(0.797) 		0.00698
(1.00) 		0.000315
(0.183) 		0.288
(1.00)
Amp Peak 13(16p11 2) 0.426
(1.00) 		0.0688
(1.00) 		0.584
(1.00) 		0.00867
(1.00) 		0.48
(1.00) 		0.000142
(0.0833) 		0.323
(1.00) 		0.000162
(0.0949) 		1
(1.00)
Amp Peak 14(16q12 1) 0.356
(1.00) 		0.0166
(1.00) 		0.493
(1.00) 		0.0112
(1.00) 		0.947
(1.00) 		0.000185
(0.108) 		0.18
(1.00) 		3e-05
(0.0179) 		0.574
(1.00)
Amp Peak 15(17q12) 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)
Amp Peak 16(17q24 1) 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)
Amp Peak 17(19p13 2) 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)
Amp Peak 18(19q13 11) 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)
Amp Peak 19(20p12 3) 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)
Amp Peak 20(20p11 23) 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)
Amp Peak 21(20p11 21) 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)
Amp Peak 22(20q11 21) 0.433
(1.00) 		0.474
(1.00) 		0.382
(1.00) 		7.66e-06
(0.00461) 		0.542
(1.00) 		0.0243
(1.00) 		0.0102
(1.00) 		0.000866
(0.493) 		0.562
(1.00)
Amp Peak 23(20q12) 0.365
(1.00) 		0.51
(1.00) 		0.324
(1.00) 		1.38e-06
(0.000832) 		0.678
(1.00) 		0.0293
(1.00) 		0.00474
(1.00) 		0.000579
(0.332) 		0.563
(1.00)
Amp Peak 24(20q13 32) 0.371
(1.00) 		0.537
(1.00) 		0.377
(1.00) 		4.8e-06
(0.00289) 		0.631
(1.00) 		0.0182
(1.00) 		0.00667
(1.00) 		0.000567
(0.326) 		0.565
(1.00)
Del Peak 1(1p36 11) 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
(0.0717) 		0.000885
(0.503) 		1
(1.00)
Del Peak 2(1p33) 0.00122
(0.684) 		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)
Del Peak 3(1p13 1) 0.0503
(1.00) 		0.891
(1.00) 		0.496
(1.00) 		0.133
(1.00) 		0.541
(1.00) 		0.00105
(0.592) 		0.000797
(0.454) 		0.00869
(1.00) 		1
(1.00)
Del Peak 4(1q43) 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)
Del Peak 5(2q37 2) 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)
Del Peak 6(3p26 1) 0.000411
(0.238) 		0.346
(1.00) 		1
(1.00) 		0.146
(1.00) 		0.0583
(1.00) 		0.0186
(1.00) 		0.000457
(0.264) 		0.000553
(0.318) 		1
(1.00)
Del Peak 7(3p14 2) 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)
Del Peak 8(3q26 31) 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)
Del Peak 9(4p16 2) 0.00024
(0.141) 		0.609
(1.00) 		0.59
(1.00) 		0.036
(1.00) 		0.67
(1.00) 		0.000256
(0.15) 		0.000266
(0.155) 		0.000587
(0.335) 		0.0247
(1.00)
Del Peak 10(4q22 1) 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)
Del Peak 11(4q35 1) 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)
Del Peak 12(5q11 2) 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)
Del Peak 13(5q21 3) 0.0728
(1.00) 		0.0679
(1.00) 		0.743
(1.00) 		0.196
(1.00) 		0.976
(1.00) 		5.3e-05
(0.0315) 		0.0201
(1.00) 		0.000579
(0.332) 		0.0223
(1.00)
Del Peak 14(5q23 1) 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)
Del Peak 15(6p25 3) 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)
Del Peak 16(6q26) 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)
Del Peak 17(7q31 1) 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)
Del Peak 18(8p23 3) 0.566
(1.00) 		0.251
(1.00) 		0.193
(1.00) 		0.0746
(1.00) 		0.165
(1.00) 		0.000318
(0.184) 		0.0225
(1.00) 		9.26e-05
(0.0548) 		0.572
(1.00)
Del Peak 19(8p22) 0.433
(1.00) 		0.104
(1.00) 		0.321
(1.00) 		0.0185
(1.00) 		0.222
(1.00) 		7.69e-06
(0.00462) 		0.00136
(0.763) 		2.17e-07
(0.000132) 		0.589
(1.00)
Del Peak 20(8p11 22) 0.412
(1.00) 		0.236
(1.00) 		0.803
(1.00) 		0.461
(1.00) 		0.342
(1.00) 		0.000914
(0.518) 		0.0887
(1.00) 		0.00266
(1.00) 		0.0973
(1.00)
Del Peak 21(8p11 21) 0.826
(1.00) 		0.377
(1.00) 		1
(1.00) 		0.633
(1.00) 		0.155
(1.00) 		0.000316
(0.184) 		0.00793
(1.00) 		0.00102
(0.577) 		0.282
(1.00)
Del Peak 22(9p21 3) 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)
Del Peak 23(10p15 3) 0.847
(1.00) 		0.434
(1.00) 		0.791
(1.00) 		0.557
(1.00) 		0.856
(1.00) 		0.00164
(0.914) 		0.00231
(1.00) 		0.0011
(0.618) 		0.0717
(1.00)
Del Peak 24(10q21 1) 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)
Del Peak 25(10q23 31) 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)
Del Peak 26(10q25 2) 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)
Del Peak 27(12p13 2) 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)
Del Peak 28(13q14 13) 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
(0.0258) 		0.835
(1.00) 		1
(1.00)
Del Peak 29(14q32 11) 0.353
(1.00) 		0.506
(1.00) 		0.674
(1.00) 		0.000917
(0.519) 		0.631
(1.00) 		0.0613
(1.00) 		0.0367
(1.00) 		0.00434
(1.00) 		0.554
(1.00)
Del Peak 30(15q11 2) 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)
Del Peak 31(15q21 1) 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)
Del Peak 32(15q22 33) 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)
Del Peak 33(16p13 3) 0.00179
(0.996) 		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)
Del Peak 34(16q23 1) 0.00129
(0.722) 		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)
Del Peak 35(17p12) 0.334
(1.00) 		0.0108
(1.00) 		0.43
(1.00) 		3.38e-06
(0.00204) 		0.869
(1.00) 		2.64e-05
(0.0157) 		0.0165
(1.00) 		1.19e-06
(0.000721) 		0.257
(1.00)
Del Peak 36(17q24 3) 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)
Del Peak 37(18p11 31) 0.869
(1.00) 		0.0199
(1.00) 		1
(1.00) 		8.39e-11
(5.13e-08) 		0.819
(1.00) 		0.0479
(1.00) 		0.00385
(1.00) 		0.00181
(1.00) 		0.251
(1.00)
Del Peak 38(18q12 2) 0.983
(1.00) 		0.0542
(1.00) 		0.421
(1.00) 		3.02e-10
(1.84e-07) 		0.838
(1.00) 		0.002
(1.00) 		0.0125
(1.00) 		0.000376
(0.218) 		0.277
(1.00)
Del Peak 39(18q21 2) 0.4
(1.00) 		0.0992
(1.00) 		0.127
(1.00) 		3.87e-09
(2.35e-06) 		0.805
(1.00) 		0.000112
(0.066) 		0.00624
(1.00) 		9.14e-06
(0.00548) 		0.299
(1.00)
Del Peak 40(18q22 1) 0.263
(1.00) 		0.176
(1.00) 		0.127
(1.00) 		4.48e-10
(2.73e-07) 		0.805
(1.00) 		0.000112
(0.066) 		0.00624
(1.00) 		2.02e-05
(0.0121) 		0.299
(1.00)
Del Peak 41(19p13 3) 0.367
(1.00) 		0.148
(1.00) 		0.67
(1.00) 		0.202
(1.00) 		0.956
(1.00) 		5.85e-05
(0.0347) 		0.0321
(1.00) 		0.00168
(0.932) 		0.36
(1.00)
Del Peak 42(20p12 1) 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)
Del Peak 43(21q11 2) 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)
Del Peak 44(22q13 32) 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)
Clustering Approach #1: 'Amp Peak 1(2q33.1) mutation analysis'

Table S1.  Description of clustering approach #1: 'Amp Peak 1(2q33.1) mutation analysis'

Cluster Labels AMP PEAK 1(2Q33.1) MUTATED AMP PEAK 1(2Q33.1) WILD-TYPE
Number of samples 79 334
Clustering Approach #2: 'Amp Peak 2(5p13.2) mutation analysis'

Table S2.  Description of clustering approach #2: 'Amp Peak 2(5p13.2) mutation analysis'

Cluster Labels AMP PEAK 2(5P13.2) MUTATED AMP PEAK 2(5P13.2) WILD-TYPE
Number of samples 81 332
Clustering Approach #3: 'Amp Peak 3(5q22.3) mutation analysis'

Table S3.  Description of clustering approach #3: 'Amp Peak 3(5q22.3) mutation analysis'

Cluster Labels AMP PEAK 3(5Q22.3) MUTATED AMP PEAK 3(5Q22.3) WILD-TYPE
Number of samples 40 373
Clustering Approach #4: 'Amp Peak 4(6p21.1) mutation analysis'

Table S4.  Description of clustering approach #4: 'Amp Peak 4(6p21.1) mutation analysis'

Cluster Labels AMP PEAK 4(6P21.1) MUTATED AMP PEAK 4(6P21.1) WILD-TYPE
Number of samples 89 324
Clustering Approach #5: 'Amp Peak 5(8p11.23) mutation analysis'

Table S5.  Description of clustering approach #5: 'Amp Peak 5(8p11.23) mutation analysis'

Cluster Labels AMP PEAK 5(8P11.23) MUTATED AMP PEAK 5(8P11.23) WILD-TYPE
Number of samples 144 269
Clustering Approach #6: 'Amp Peak 6(8p11.21) mutation analysis'

Table S6.  Description of clustering approach #6: 'Amp Peak 6(8p11.21) mutation analysis'

Cluster Labels AMP PEAK 6(8P11.21) MUTATED AMP PEAK 6(8P11.21) WILD-TYPE
Number of samples 173 240
Clustering Approach #7: 'Amp Peak 7(8q12.1) mutation analysis'

Table S7.  Description of clustering approach #7: 'Amp Peak 7(8q12.1) mutation analysis'

Cluster Labels AMP PEAK 7(8Q12.1) MUTATED AMP PEAK 7(8Q12.1) WILD-TYPE
Number of samples 215 198
Clustering Approach #8: 'Amp Peak 8(8q24.21) mutation analysis'

Table S8.  Description of clustering approach #8: 'Amp Peak 8(8q24.21) mutation analysis'

Cluster Labels AMP PEAK 8(8Q24.21) MUTATED AMP PEAK 8(8Q24.21) WILD-TYPE
Number of samples 239 174
Clustering Approach #9: 'Amp Peak 9(11p15.5) mutation analysis'

Table S9.  Description of clustering approach #9: 'Amp Peak 9(11p15.5) mutation analysis'

Cluster Labels AMP PEAK 9(11P15.5) MUTATED AMP PEAK 9(11P15.5) WILD-TYPE
Number of samples 86 327
Clustering Approach #10: 'Amp Peak 10(12p13.33) mutation analysis'

Table S10.  Description of clustering approach #10: 'Amp Peak 10(12p13.33) mutation analysis'

Cluster Labels AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
Number of samples 104 309
Clustering Approach #11: 'Amp Peak 11(13q12.13) mutation analysis'

Table S11.  Description of clustering approach #11: 'Amp Peak 11(13q12.13) mutation analysis'

Cluster Labels AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE
Number of samples 250 163
'Amp Peak 11(13q12.13) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.87e-07 (Fisher's exact test), Q value = 0.00054

Table S12.  Clustering Approach #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

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

Clustering Approach #12: 'Amp Peak 12(13q22.1) mutation analysis'

Table S13.  Description of clustering approach #12: 'Amp Peak 12(13q22.1) mutation analysis'

Cluster Labels AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE
Number of samples 254 159
'Amp Peak 12(13q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.13e-06 (Fisher's exact test), Q value = 0.0049

Table S14.  Clustering Approach #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

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

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

P value = 0.000315 (Fisher's exact test), Q value = 0.18

Table S15.  Clustering Approach #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

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

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

Clustering Approach #13: 'Amp Peak 13(16p11.2) mutation analysis'

Table S16.  Description of clustering approach #13: 'Amp Peak 13(16p11.2) mutation analysis'

Cluster Labels AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE
Number of samples 116 297
'Amp Peak 13(16p11.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000142 (Fisher's exact test), Q value = 0.083

Table S17.  Clustering Approach #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

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

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

P value = 0.000162 (Fisher's exact test), Q value = 0.095

Table S18.  Clustering Approach #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

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

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

Clustering Approach #14: 'Amp Peak 14(16q12.1) mutation analysis'

Table S19.  Description of clustering approach #14: 'Amp Peak 14(16q12.1) mutation analysis'

Cluster Labels AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE
Number of samples 102 311
'Amp Peak 14(16q12.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000185 (Fisher's exact test), Q value = 0.11

Table S20.  Clustering Approach #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

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

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

P value = 3e-05 (Fisher's exact test), Q value = 0.018

Table S21.  Clustering Approach #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

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

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

Clustering Approach #15: 'Amp Peak 15(17q12) mutation analysis'

Table S22.  Description of clustering approach #15: 'Amp Peak 15(17q12) mutation analysis'

Cluster Labels AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE
Number of samples 101 312
Clustering Approach #16: 'Amp Peak 16(17q24.1) mutation analysis'

Table S23.  Description of clustering approach #16: 'Amp Peak 16(17q24.1) mutation analysis'

Cluster Labels AMP PEAK 16(17Q24.1) MUTATED AMP PEAK 16(17Q24.1) WILD-TYPE
Number of samples 92 321
Clustering Approach #17: 'Amp Peak 17(19p13.2) mutation analysis'

Table S24.  Description of clustering approach #17: 'Amp Peak 17(19p13.2) mutation analysis'

Cluster Labels AMP PEAK 17(19P13.2) MUTATED AMP PEAK 17(19P13.2) WILD-TYPE
Number of samples 65 348
Clustering Approach #18: 'Amp Peak 18(19q13.11) mutation analysis'

Table S25.  Description of clustering approach #18: 'Amp Peak 18(19q13.11) mutation analysis'

Cluster Labels AMP PEAK 18(19Q13.11) MUTATED AMP PEAK 18(19Q13.11) WILD-TYPE
Number of samples 83 330
Clustering Approach #19: 'Amp Peak 19(20p12.3) mutation analysis'

Table S26.  Description of clustering approach #19: 'Amp Peak 19(20p12.3) mutation analysis'

Cluster Labels AMP PEAK 19(20P12.3) MUTATED AMP PEAK 19(20P12.3) WILD-TYPE
Number of samples 184 229
Clustering Approach #20: 'Amp Peak 20(20p11.23) mutation analysis'

Table S27.  Description of clustering approach #20: 'Amp Peak 20(20p11.23) mutation analysis'

Cluster Labels AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE
Number of samples 205 208
Clustering Approach #21: 'Amp Peak 21(20p11.21) mutation analysis'

Table S28.  Description of clustering approach #21: 'Amp Peak 21(20p11.21) mutation analysis'

Cluster Labels AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE
Number of samples 230 183
Clustering Approach #22: 'Amp Peak 22(20q11.21) mutation analysis'

Table S29.  Description of clustering approach #22: 'Amp Peak 22(20q11.21) mutation analysis'

Cluster Labels AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
Number of samples 296 117
'Amp Peak 22(20q11.21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.66e-06 (Fisher's exact test), Q value = 0.0046

Table S30.  Clustering Approach #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

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

Clustering Approach #23: 'Amp Peak 23(20q12) mutation analysis'

Table S31.  Description of clustering approach #23: 'Amp Peak 23(20q12) mutation analysis'

Cluster Labels AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE
Number of samples 297 116
'Amp Peak 23(20q12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.00083

Table S32.  Clustering Approach #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

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

Clustering Approach #24: 'Amp Peak 24(20q13.32) mutation analysis'

Table S33.  Description of clustering approach #24: 'Amp Peak 24(20q13.32) mutation analysis'

Cluster Labels AMP PEAK 24(20Q13.32) MUTATED AMP PEAK 24(20Q13.32) WILD-TYPE
Number of samples 300 113
'Amp Peak 24(20q13.32) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.8e-06 (Fisher's exact test), Q value = 0.0029

Table S34.  Clustering Approach #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

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

Clustering Approach #25: 'Del Peak 1(1p36.11) mutation analysis'

Table S35.  Description of clustering approach #25: 'Del Peak 1(1p36.11) mutation analysis'

Cluster Labels DEL PEAK 1(1P36.11) MUTATED DEL PEAK 1(1P36.11) WILD-TYPE
Number of samples 150 263
'Del Peak 1(1p36.11) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000122 (Chi-square test), Q value = 0.072

Table S36.  Clustering Approach #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

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

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

Clustering Approach #26: 'Del Peak 2(1p33) mutation analysis'

Table S37.  Description of clustering approach #26: 'Del Peak 2(1p33) mutation analysis'

Cluster Labels DEL PEAK 2(1P33) MUTATED DEL PEAK 2(1P33) WILD-TYPE
Number of samples 107 306
Clustering Approach #27: 'Del Peak 3(1p13.1) mutation analysis'

Table S38.  Description of clustering approach #27: 'Del Peak 3(1p13.1) mutation analysis'

Cluster Labels DEL PEAK 3(1P13.1) MUTATED DEL PEAK 3(1P13.1) WILD-TYPE
Number of samples 103 310
Clustering Approach #28: 'Del Peak 4(1q43) mutation analysis'

Table S39.  Description of clustering approach #28: 'Del Peak 4(1q43) mutation analysis'

Cluster Labels DEL PEAK 4(1Q43) MUTATED DEL PEAK 4(1Q43) WILD-TYPE
Number of samples 44 369
Clustering Approach #29: 'Del Peak 5(2q37.2) mutation analysis'

Table S40.  Description of clustering approach #29: 'Del Peak 5(2q37.2) mutation analysis'

Cluster Labels DEL PEAK 5(2Q37.2) MUTATED DEL PEAK 5(2Q37.2) WILD-TYPE
Number of samples 21 392
Clustering Approach #30: 'Del Peak 6(3p26.1) mutation analysis'

Table S41.  Description of clustering approach #30: 'Del Peak 6(3p26.1) mutation analysis'

Cluster Labels DEL PEAK 6(3P26.1) MUTATED DEL PEAK 6(3P26.1) WILD-TYPE
Number of samples 60 353
'Del Peak 6(3p26.1) mutation analysis' versus 'Time to Death'

P value = 0.000411 (logrank test), Q value = 0.24

Table S42.  Clustering Approach #30: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 319 49 0.1 - 135.5 (7.7)
DEL PEAK 6(3P26.1) MUTATED 43 8 0.2 - 16.9 (5.0)
DEL PEAK 6(3P26.1) WILD-TYPE 276 41 0.1 - 135.5 (8.2)

Figure S12.  Get High-res Image Clustering Approach #30: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

Clustering Approach #31: 'Del Peak 7(3p14.2) mutation analysis'

Table S43.  Description of clustering approach #31: 'Del Peak 7(3p14.2) mutation analysis'

Cluster Labels DEL PEAK 7(3P14.2) MUTATED DEL PEAK 7(3P14.2) WILD-TYPE
Number of samples 75 338
Clustering Approach #32: 'Del Peak 8(3q26.31) mutation analysis'

Table S44.  Description of clustering approach #32: 'Del Peak 8(3q26.31) mutation analysis'

Cluster Labels DEL PEAK 8(3Q26.31) MUTATED DEL PEAK 8(3Q26.31) WILD-TYPE
Number of samples 39 374
Clustering Approach #33: 'Del Peak 9(4p16.2) mutation analysis'

Table S45.  Description of clustering approach #33: 'Del Peak 9(4p16.2) mutation analysis'

Cluster Labels DEL PEAK 9(4P16.2) MUTATED DEL PEAK 9(4P16.2) WILD-TYPE
Number of samples 121 292
'Del Peak 9(4p16.2) mutation analysis' versus 'Time to Death'

P value = 0.00024 (logrank test), Q value = 0.14

Table S46.  Clustering Approach #33: 'Del Peak 9(4p16.2) mutation analysis' 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) MUTATED 89 20 0.2 - 87.8 (7.6)
DEL PEAK 9(4P16.2) WILD-TYPE 230 29 0.1 - 135.5 (8.0)

Figure S13.  Get High-res Image Clustering Approach #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

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

P value = 0.000256 (Fisher's exact test), Q value = 0.15

Table S47.  Clustering Approach #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

Figure S14.  Get High-res Image Clustering Approach #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

P value = 0.000266 (Chi-square test), Q value = 0.16

Table S48.  Clustering Approach #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

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

Figure S15.  Get High-res Image Clustering Approach #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

Clustering Approach #34: 'Del Peak 10(4q22.1) mutation analysis'

Table S49.  Description of clustering approach #34: 'Del Peak 10(4q22.1) mutation analysis'

Cluster Labels DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
Number of samples 126 287
Clustering Approach #35: 'Del Peak 11(4q35.1) mutation analysis'

Table S50.  Description of clustering approach #35: 'Del Peak 11(4q35.1) mutation analysis'

Cluster Labels DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
Number of samples 137 276
Clustering Approach #36: 'Del Peak 12(5q11.2) mutation analysis'

Table S51.  Description of clustering approach #36: 'Del Peak 12(5q11.2) mutation analysis'

Cluster Labels DEL PEAK 12(5Q11.2) MUTATED DEL PEAK 12(5Q11.2) WILD-TYPE
Number of samples 91 322
Clustering Approach #37: 'Del Peak 13(5q21.3) mutation analysis'

Table S52.  Description of clustering approach #37: 'Del Peak 13(5q21.3) mutation analysis'

Cluster Labels DEL PEAK 13(5Q21.3) MUTATED DEL PEAK 13(5Q21.3) WILD-TYPE
Number of samples 117 296
'Del Peak 13(5q21.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 5.3e-05 (Fisher's exact test), Q value = 0.031

Table S53.  Clustering Approach #37: 'Del Peak 13(5q21.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

Figure S16.  Get High-res Image Clustering Approach #37: 'Del Peak 13(5q21.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

Clustering Approach #38: 'Del Peak 14(5q23.1) mutation analysis'

Table S54.  Description of clustering approach #38: 'Del Peak 14(5q23.1) mutation analysis'

Cluster Labels DEL PEAK 14(5Q23.1) MUTATED DEL PEAK 14(5Q23.1) WILD-TYPE
Number of samples 107 306
Clustering Approach #39: 'Del Peak 15(6p25.3) mutation analysis'

Table S55.  Description of clustering approach #39: 'Del Peak 15(6p25.3) mutation analysis'

Cluster Labels DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
Number of samples 54 359
Clustering Approach #40: 'Del Peak 16(6q26) mutation analysis'

Table S56.  Description of clustering approach #40: 'Del Peak 16(6q26) mutation analysis'

Cluster Labels DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
Number of samples 60 353
Clustering Approach #41: 'Del Peak 17(7q31.1) mutation analysis'

Table S57.  Description of clustering approach #41: 'Del Peak 17(7q31.1) mutation analysis'

Cluster Labels DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
Number of samples 11 402
Clustering Approach #42: 'Del Peak 18(8p23.3) mutation analysis'

Table S58.  Description of clustering approach #42: 'Del Peak 18(8p23.3) mutation analysis'

Cluster Labels DEL PEAK 18(8P23.3) MUTATED DEL PEAK 18(8P23.3) WILD-TYPE
Number of samples 171 242
'Del Peak 18(8p23.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000318 (Fisher's exact test), Q value = 0.18

Table S59.  Clustering Approach #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

Figure S17.  Get High-res Image Clustering Approach #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

P value = 9.26e-05 (Fisher's exact test), Q value = 0.055

Table S60.  Clustering Approach #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

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

Figure S18.  Get High-res Image Clustering Approach #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

Clustering Approach #43: 'Del Peak 19(8p22) mutation analysis'

Table S61.  Description of clustering approach #43: 'Del Peak 19(8p22) mutation analysis'

Cluster Labels DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
Number of samples 185 228
'Del Peak 19(8p22) mutation analysis' versus 'PATHOLOGY.N'

P value = 7.69e-06 (Fisher's exact test), Q value = 0.0046

Table S62.  Clustering Approach #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

Figure S19.  Get High-res Image Clustering Approach #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

P value = 2.17e-07 (Fisher's exact test), Q value = 0.00013

Table S63.  Clustering Approach #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

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

Figure S20.  Get High-res Image Clustering Approach #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

Clustering Approach #44: 'Del Peak 20(8p11.22) mutation analysis'

Table S64.  Description of clustering approach #44: 'Del Peak 20(8p11.22) mutation analysis'

Cluster Labels DEL PEAK 20(8P11.22) MUTATED DEL PEAK 20(8P11.22) WILD-TYPE
Number of samples 80 333
Clustering Approach #45: 'Del Peak 21(8p11.21) mutation analysis'

Table S65.  Description of clustering approach #45: 'Del Peak 21(8p11.21) mutation analysis'

Cluster Labels DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE
Number of samples 43 370
'Del Peak 21(8p11.21) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000316 (Fisher's exact test), Q value = 0.18

Table S66.  Clustering Approach #45: 'Del Peak 21(8p11.21) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

Figure S21.  Get High-res Image Clustering Approach #45: 'Del Peak 21(8p11.21) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

Clustering Approach #46: 'Del Peak 22(9p21.3) mutation analysis'

Table S67.  Description of clustering approach #46: 'Del Peak 22(9p21.3) mutation analysis'

Cluster Labels DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
Number of samples 56 357
Clustering Approach #47: 'Del Peak 23(10p15.3) mutation analysis'

Table S68.  Description of clustering approach #47: 'Del Peak 23(10p15.3) mutation analysis'

Cluster Labels DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
Number of samples 68 345
Clustering Approach #48: 'Del Peak 24(10q21.1) mutation analysis'

Table S69.  Description of clustering approach #48: 'Del Peak 24(10q21.1) mutation analysis'

Cluster Labels DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
Number of samples 82 331
Clustering Approach #49: 'Del Peak 25(10q23.31) mutation analysis'

Table S70.  Description of clustering approach #49: 'Del Peak 25(10q23.31) mutation analysis'

Cluster Labels DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
Number of samples 94 319
Clustering Approach #50: 'Del Peak 26(10q25.2) mutation analysis'

Table S71.  Description of clustering approach #50: 'Del Peak 26(10q25.2) mutation analysis'

Cluster Labels DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
Number of samples 93 320
Clustering Approach #51: 'Del Peak 27(12p13.2) mutation analysis'

Table S72.  Description of clustering approach #51: 'Del Peak 27(12p13.2) mutation analysis'

Cluster Labels DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
Number of samples 44 369
Clustering Approach #52: 'Del Peak 28(13q14.13) mutation analysis'

Table S73.  Description of clustering approach #52: 'Del Peak 28(13q14.13) mutation analysis'

Cluster Labels DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
Number of samples 18 395
'Del Peak 28(13q14.13) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 4.33e-05 (Chi-square test), Q value = 0.026

Table S74.  Clustering Approach #52: 'Del Peak 28(13q14.13) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

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

Figure S22.  Get High-res Image Clustering Approach #52: 'Del Peak 28(13q14.13) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

Clustering Approach #53: 'Del Peak 29(14q32.11) mutation analysis'

Table S75.  Description of clustering approach #53: 'Del Peak 29(14q32.11) mutation analysis'

Cluster Labels DEL PEAK 29(14Q32.11) MUTATED DEL PEAK 29(14Q32.11) WILD-TYPE
Number of samples 133 280
Clustering Approach #54: 'Del Peak 30(15q11.2) mutation analysis'

Table S76.  Description of clustering approach #54: 'Del Peak 30(15q11.2) mutation analysis'

Cluster Labels DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
Number of samples 160 253
Clustering Approach #55: 'Del Peak 31(15q21.1) mutation analysis'

Table S77.  Description of clustering approach #55: 'Del Peak 31(15q21.1) mutation analysis'

Cluster Labels DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
Number of samples 151 262
Clustering Approach #56: 'Del Peak 32(15q22.33) mutation analysis'

Table S78.  Description of clustering approach #56: 'Del Peak 32(15q22.33) mutation analysis'

Cluster Labels DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
Number of samples 145 268
Clustering Approach #57: 'Del Peak 33(16p13.3) mutation analysis'

Table S79.  Description of clustering approach #57: 'Del Peak 33(16p13.3) mutation analysis'

Cluster Labels DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
Number of samples 45 368
Clustering Approach #58: 'Del Peak 34(16q23.1) mutation analysis'

Table S80.  Description of clustering approach #58: 'Del Peak 34(16q23.1) mutation analysis'

Cluster Labels DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
Number of samples 49 364
Clustering Approach #59: 'Del Peak 35(17p12) mutation analysis'

Table S81.  Description of clustering approach #59: 'Del Peak 35(17p12) mutation analysis'

Cluster Labels DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
Number of samples 229 184
'Del Peak 35(17p12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.38e-06 (Fisher's exact test), Q value = 0.002

Table S82.  Clustering Approach #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

Figure S23.  Get High-res Image Clustering Approach #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

P value = 2.64e-05 (Fisher's exact test), Q value = 0.016

Table S83.  Clustering Approach #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

Figure S24.  Get High-res Image Clustering Approach #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

P value = 1.19e-06 (Fisher's exact test), Q value = 0.00072

Table S84.  Clustering Approach #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

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

Figure S25.  Get High-res Image Clustering Approach #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

Clustering Approach #60: 'Del Peak 36(17q24.3) mutation analysis'

Table S85.  Description of clustering approach #60: 'Del Peak 36(17q24.3) mutation analysis'

Cluster Labels DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
Number of samples 59 354
Clustering Approach #61: 'Del Peak 37(18p11.31) mutation analysis'

Table S86.  Description of clustering approach #61: 'Del Peak 37(18p11.31) mutation analysis'

Cluster Labels DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
Number of samples 220 193
'Del Peak 37(18p11.31) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.39e-11 (Fisher's exact test), Q value = 5.1e-08

Table S87.  Clustering Approach #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

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

Clustering Approach #62: 'Del Peak 38(18q12.2) mutation analysis'

Table S88.  Description of clustering approach #62: 'Del Peak 38(18q12.2) mutation analysis'

Cluster Labels DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
Number of samples 247 166
'Del Peak 38(18q12.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.02e-10 (Fisher's exact test), Q value = 1.8e-07

Table S89.  Clustering Approach #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

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

'Del Peak 38(18q12.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000376 (Fisher's exact test), Q value = 0.22

Table S90.  Clustering Approach #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients I II III IV
ALL 67 157 116 56
DEL PEAK 38(18Q12.2) MUTATED 34 78 78 43
DEL PEAK 38(18Q12.2) WILD-TYPE 33 79 38 13

Figure S28.  Get High-res Image Clustering Approach #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

Clustering Approach #63: 'Del Peak 39(18q21.2) mutation analysis'

Table S91.  Description of clustering approach #63: 'Del Peak 39(18q21.2) mutation analysis'

Cluster Labels DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
Number of samples 260 153
'Del Peak 39(18q21.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.87e-09 (Fisher's exact test), Q value = 2.4e-06

Table S92.  Clustering Approach #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

Figure S29.  Get High-res Image Clustering Approach #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

P value = 0.000112 (Fisher's exact test), Q value = 0.066

Table S93.  Clustering Approach #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

Figure S30.  Get High-res Image Clustering Approach #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

P value = 9.14e-06 (Fisher's exact test), Q value = 0.0055

Table S94.  Clustering Approach #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

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

Figure S31.  Get High-res Image Clustering Approach #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

Clustering Approach #64: 'Del Peak 40(18q22.1) mutation analysis'

Table S95.  Description of clustering approach #64: 'Del Peak 40(18q22.1) mutation analysis'

Cluster Labels DEL PEAK 40(18Q22.1) MUTATED DEL PEAK 40(18Q22.1) WILD-TYPE
Number of samples 260 153
'Del Peak 40(18q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.48e-10 (Fisher's exact test), Q value = 2.7e-07

Table S96.  Clustering Approach #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

Figure S32.  Get High-res Image Clustering Approach #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

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

P value = 0.000112 (Fisher's exact test), Q value = 0.066

Table S97.  Clustering Approach #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

Figure S33.  Get High-res Image Clustering Approach #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

P value = 2.02e-05 (Fisher's exact test), Q value = 0.012

Table S98.  Clustering Approach #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

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

Figure S34.  Get High-res Image Clustering Approach #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

Clustering Approach #65: 'Del Peak 41(19p13.3) mutation analysis'

Table S99.  Description of clustering approach #65: 'Del Peak 41(19p13.3) mutation analysis'

Cluster Labels DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
Number of samples 57 356
'Del Peak 41(19p13.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 5.85e-05 (Fisher's exact test), Q value = 0.035

Table S100.  Clustering Approach #65: 'Del Peak 41(19p13.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

Figure S35.  Get High-res Image Clustering Approach #65: 'Del Peak 41(19p13.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

Clustering Approach #66: 'Del Peak 42(20p12.1) mutation analysis'

Table S101.  Description of clustering approach #66: 'Del Peak 42(20p12.1) mutation analysis'

Cluster Labels DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
Number of samples 79 334
Clustering Approach #67: 'Del Peak 43(21q11.2) mutation analysis'

Table S102.  Description of clustering approach #67: 'Del Peak 43(21q11.2) mutation analysis'

Cluster Labels DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
Number of samples 125 288
Clustering Approach #68: 'Del Peak 44(22q13.32) mutation analysis'

Table S103.  Description of clustering approach #68: 'Del Peak 44(22q13.32) mutation analysis'

Cluster Labels DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
Number of samples 138 275
Methods & Data
Input

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

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

  • Number of patients = 413

  • Number of clustering approaches = 68

  • Number of selected clinical features = 9

  • Exclude small clusters that include fewer than K patients, 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 two tumor subtypes using 't.test' function in R

Fisher's exact test

For binary clinical features, 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.

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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