Correlation between copy number variation genes (focal) and selected clinical features
Colon Adenocarcinoma (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C1DZ06G6
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1DZ06G6
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.

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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)
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