Colon/Rectal Adenocarcinoma: Correlation between copy number variation genes and selected clinical features
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

Testing the association between copy number variation of 75 peak regions and 10 clinical features across 575 patients, 53 significant findings detected with Q value < 0.25.

- Amp Peak 5(6p21.1) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.

- Amp Peak 6(7p21.3) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Amp Peak 14(13q12.13) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Amp Peak 15(13q12.2) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Amp Peak 16(13q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'PATHOLOGY.N'.

- Amp Peak 18(16p11.2) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.

- Amp Peak 24(20p11.21) cnvs correlated to 'HISTOLOGICAL.TYPE'.

- Amp Peak 25(20q11.21) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- Amp Peak 26(20q12) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- Amp Peak 27(20q13.32) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- Del Peak 10(4p16.1) cnvs correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 18(8p23.2) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Del Peak 19(8p22) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Del Peak 30(14q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE'.

- Del Peak 34(16p13.3) cnvs correlated to 'Time to Death'.

- Del Peak 36(17p12) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Del Peak 38(18p11.31) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- Del Peak 39(18q12.2) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Del Peak 40(18q21.2) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Del Peak 41(18q22.1) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Del Peak 42(19p13.3) cnvs correlated to 'PATHOLOGY.N'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 75 regions and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 53 significant findings detected.

|  | Clinical Features | Time to Death | AGE | PRIMARY SITE OF DISEASE | GENDER | HISTOLOGICAL TYPE | PATHOLOGY T | PATHOLOGY N | PATHOLOGICSPREAD(M) | TUMOR STAGE | RADIATIONS RADIATION REGIMENINDICATION
| nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact 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
Del Peak 18(8p23 2) | 272 (47%) | 303 | 0.619 (1.00) | 0.205 (1.00) | 2.4e-05 (0.0173) | 0.18 (1.00) | 2.8e-05 (0.0201) | 0.0809 (1.00) | 2.71e-05 (0.0195) | 0.00989 (1.00) | 3.34e-05 (0.0239) | 0.0155 (1.00)
Del Peak 39(18q12 2) | 386 (67%) | 189 | 0.942 (1.00) | 0.0817 (1.00) | 1.57e-09 (1.16e-06) | 0.477 (1.00) | 5.64e-18 (4.23e-15) | 0.424 (1.00) | 0.000131 (0.0919) | 0.00447 (1.00) | 6.7e-05 (0.0477) | 0.034 (1.00)
Del Peak 40(18q21 2) | 403 (70%) | 172 | 0.481 (1.00) | 0.0823 (1.00) | 1.07e-09 (7.94e-07) | 0.145 (1.00) | 2.57e-16 (1.92e-13) | 0.314 (1.00) | 2.01e-06 (0.00147) | 0.00162 (1.00) | 3.94e-07 (0.00029) | 0.0637 (1.00)
Del Peak 41(18q22 1) | 398 (69%) | 177 | 0.332 (1.00) | 0.221 (1.00) | 1.94e-07 (0.000143) | 0.239 (1.00) | 1.41e-15 (1.05e-12) | 0.443 (1.00) | 1.1e-05 (0.00795) | 0.00238 (1.00) | 4.52e-06 (0.0033) | 0.0632 (1.00)
Amp Peak 6(7p21 3) | 337 (59%) | 238 | 0.304 (1.00) | 0.103 (1.00) | 0.0292 (1.00) | 0.734 (1.00) | 0.000219 (0.153) | 0.889 (1.00) | 1.22e-05 (0.00884) | 0.0274 (1.00) | 4.31e-06 (0.00314) | 0.0882 (1.00)
Amp Peak 14(13q12 13) | 371 (65%) | 204 | 0.126 (1.00) | 0.314 (1.00) | 0.00246 (1.00) | 0.727 (1.00) | 1.03e-09 (7.68e-07) | 0.564 (1.00) | 3.94e-05 (0.0281) | 0.0101 (1.00) | 7.37e-05 (0.0523) | 1 (1.00)
Amp Peak 15(13q12 2) | 366 (64%) | 209 | 0.101 (1.00) | 0.239 (1.00) | 0.00188 (1.00) | 0.543 (1.00) | 2.33e-09 (1.72e-06) | 0.53 (1.00) | 9.29e-05 (0.0657) | 0.023 (1.00) | 0.000181 (0.127) | 1 (1.00)
Amp Peak 25(20q11 21) | 439 (76%) | 136 | 0.317 (1.00) | 0.823 (1.00) | 9.13e-06 (0.00664) | 0.376 (1.00) | 5.89e-12 (4.39e-09) | 0.513 (1.00) | 0.00142 (0.946) | 0.00533 (1.00) | 0.000105 (0.0738) | 0.693 (1.00)
Amp Peak 26(20q12) | 441 (77%) | 134 | 0.274 (1.00) | 0.726 (1.00) | 4.74e-06 (0.00345) | 0.374 (1.00) | 3.83e-13 (2.85e-10) | 0.612 (1.00) | 0.001 (0.683) | 0.00129 (0.869) | 4e-05 (0.0285) | 0.692 (1.00)
Amp Peak 27(20q13 32) | 444 (77%) | 131 | 0.369 (1.00) | 0.658 (1.00) | 2.18e-05 (0.0158) | 0.551 (1.00) | 6.45e-12 (4.8e-09) | 0.588 (1.00) | 0.0016 (1.00) | 0.00424 (1.00) | 0.000128 (0.0901) | 0.692 (1.00)
Del Peak 19(8p22) | 285 (50%) | 290 | 0.597 (1.00) | 0.317 (1.00) | 0.000379 (0.265) | 0.403 (1.00) | 0.000248 (0.173) | 0.075 (1.00) | 1.96e-06 (0.00144) | 0.00381 (1.00) | 1.22e-06 (0.000897) | 0.0196 (1.00)
Del Peak 36(17p12) | 343 (60%) | 232 | 0.656 (1.00) | 0.0983 (1.00) | 0.00169 (1.00) | 0.609 (1.00) | 5.98e-08 (4.41e-05) | 0.422 (1.00) | 0.000119 (0.0839) | 0.041 (1.00) | 3.09e-05 (0.0222) | 0.325 (1.00)
Amp Peak 5(6p21 1) | 146 (25%) | 429 | 0.489 (1.00) | 0.682 (1.00) | 0.0314 (1.00) | 0.15 (1.00) | 0.00234 (1.00) | 0.214 (1.00) | 3.15e-05 (0.0226) | 0.109 (1.00) | 0.000322 (0.225) | 0.00136 (0.912)
Amp Peak 16(13q22 1) | 371 (65%) | 204 | 0.0454 (1.00) | 0.444 (1.00) | 0.0249 (1.00) | 0.221 (1.00) | 2.84e-08 (2.1e-05) | 0.737 (1.00) | 0.000126 (0.0887) | 0.024 (1.00) | 0.000595 (0.412) | 0.503 (1.00)
Amp Peak 18(16p11 2) | 161 (28%) | 414 | 0.838 (1.00) | 0.26 (1.00) | 0.918 (1.00) | 0.71 (1.00) | 0.00229 (1.00) | 0.721 (1.00) | 5.86e-05 (0.0417) | 0.111 (1.00) | 8.31e-05 (0.0588) | 0.715 (1.00)
Del Peak 38(18p11 31) | 341 (59%) | 234 | 0.98 (1.00) | 0.059 (1.00) | 1.82e-06 (0.00134) | 1 (1.00) | 1.11e-16 (8.35e-14) | 0.886 (1.00) | 0.0108 (1.00) | 0.000584 (0.406) | 0.000888 (0.607) | 0.322 (1.00)
Amp Peak 24(20p11 21) | 339 (59%) | 236 | 0.808 (1.00) | 0.709 (1.00) | 0.00784 (1.00) | 0.0413 (1.00) | 1.08e-05 (0.00782) | 0.886 (1.00) | 0.381 (1.00) | 0.00312 (1.00) | 0.0517 (1.00) | 0.32 (1.00)
Del Peak 10(4p16 1) | 182 (32%) | 393 | 0.0406 (1.00) | 0.954 (1.00) | 0.0561 (1.00) | 0.128 (1.00) | 0.0276 (1.00) | 0.988 (1.00) | 0.000554 (0.385) | 0.0131 (1.00) | 0.00162 (1.00) | 2.78e-05 (0.02)
Del Peak 30(14q22 1) | 185 (32%) | 390 | 0.208 (1.00) | 0.233 (1.00) | 0.0212 (1.00) | 0.421 (1.00) | 1.08e-06 (0.000797) | 0.777 (1.00) | 0.00353 (1.00) | 0.145 (1.00) | 0.174 (1.00) | 0.725 (1.00)
Del Peak 34(16p13 3) | 58 (10%) | 517 | 4.34e-05 (0.031) | 0.254 (1.00) | 0.359 (1.00) | 0.89 (1.00) | 0.422 (1.00) | 0.0652 (1.00) | 0.133 (1.00) | 0.381 (1.00) | 0.099 (1.00) | 0.609 (1.00)
Del Peak 42(19p13 3) | 92 (16%) | 483 | 0.406 (1.00) | 0.183 (1.00) | 0.0305 (1.00) | 0.733 (1.00) | 0.0672 (1.00) | 0.411 (1.00) | 7.59e-05 (0.0538) | 0.0275 (1.00) | 0.00301 (1.00) | 0.641 (1.00)
Amp Peak 1(1q31 1) | 134 (23%) | 441 | 0.466 (1.00) | 0.292 (1.00) | 0.0268 (1.00) | 0.236 (1.00) | 0.0928 (1.00) | 0.381 (1.00) | 0.0533 (1.00) | 0.175 (1.00) | 0.0341 (1.00) | 0.0357 (1.00)
Amp Peak 2(2q33 1) | 123 (21%) | 452 | 0.135 (1.00) | 0.385 (1.00) | 0.031 (1.00) | 1 (1.00) | 0.00359 (1.00) | 0.684 (1.00) | 0.00128 (0.866) | 0.541 (1.00) | 0.0223 (1.00) | 0.103 (1.00)
Amp Peak 3(5p12) | 107 (19%) | 468 | 0.0162 (1.00) | 0.372 (1.00) | 0.151 (1.00) | 0.748 (1.00) | 0.0551 (1.00) | 0.398 (1.00) | 0.0424 (1.00) | 0.354 (1.00) | 0.19 (1.00) | 0.379 (1.00)
Amp Peak 4(5q22 3) | 59 (10%) | 516 | 0.75 (1.00) | 0.865 (1.00) | 0.445 (1.00) | 0.891 (1.00) | 0.315 (1.00) | 0.908 (1.00) | 0.174 (1.00) | 0.032 (1.00) | 0.118 (1.00) | 1 (1.00)
Amp Peak 7(8p11 23) | 196 (34%) | 379 | 0.472 (1.00) | 0.752 (1.00) | 0.625 (1.00) | 0.482 (1.00) | 0.232 (1.00) | 0.409 (1.00) | 0.51 (1.00) | 0.413 (1.00) | 0.881 (1.00) | 0.498 (1.00)
Amp Peak 8(8p11 21) | 238 (41%) | 337 | 0.633 (1.00) | 0.597 (1.00) | 0.636 (1.00) | 0.204 (1.00) | 0.12 (1.00) | 0.504 (1.00) | 0.337 (1.00) | 0.305 (1.00) | 0.479 (1.00) | 0.742 (1.00)
Amp Peak 9(8q12 1) | 309 (54%) | 266 | 0.907 (1.00) | 0.19 (1.00) | 0.303 (1.00) | 0.615 (1.00) | 0.00904 (1.00) | 0.127 (1.00) | 0.0851 (1.00) | 0.0256 (1.00) | 0.0726 (1.00) | 0.0423 (1.00)
Amp Peak 10(8q24 21) | 345 (60%) | 230 | 0.545 (1.00) | 0.236 (1.00) | 0.0863 (1.00) | 0.394 (1.00) | 0.0111 (1.00) | 0.144 (1.00) | 0.173 (1.00) | 0.0551 (1.00) | 0.234 (1.00) | 0.0931 (1.00)
Amp Peak 11(10q22 3) | 35 (6%) | 540 | 0.819 (1.00) | 0.303 (1.00) | 1 (1.00) | 0.487 (1.00) | 0.952 (1.00) | 0.137 (1.00) | 0.00778 (1.00) | 0.912 (1.00) | 0.114 (1.00) | 0.434 (1.00)
Amp Peak 12(11p15 5) | 129 (22%) | 446 | 0.709 (1.00) | 0.0608 (1.00) | 0.145 (1.00) | 0.549 (1.00) | 0.00139 (0.931) | 0.296 (1.00) | 0.71 (1.00) | 0.385 (1.00) | 0.817 (1.00) | 0.12 (1.00)
Amp Peak 13(12p13 32) | 144 (25%) | 431 | 0.26 (1.00) | 0.0696 (1.00) | 0.829 (1.00) | 0.5 (1.00) | 0.353 (1.00) | 0.383 (1.00) | 0.0531 (1.00) | 0.0859 (1.00) | 0.0619 (1.00) | 0.698 (1.00)
Amp Peak 17(15q26 1) | 43 (7%) | 532 | 0.0824 (1.00) | 0.753 (1.00) | 0.291 (1.00) | 0.0582 (1.00) | 0.435 (1.00) | 0.281 (1.00) | 0.00407 (1.00) | 0.649 (1.00) | 0.194 (1.00) | 0.141 (1.00)
Amp Peak 19(17q12) | 144 (25%) | 431 | 0.489 (1.00) | 0.363 (1.00) | 0.591 (1.00) | 0.101 (1.00) | 0.459 (1.00) | 0.42 (1.00) | 0.151 (1.00) | 0.0117 (1.00) | 0.0157 (1.00) | 0.462 (1.00)
Amp Peak 20(17q24 1) | 128 (22%) | 447 | 0.0431 (1.00) | 0.245 (1.00) | 0.911 (1.00) | 0.617 (1.00) | 0.087 (1.00) | 0.774 (1.00) | 0.896 (1.00) | 0.0549 (1.00) | 0.22 (1.00) | 0.691 (1.00)
Amp Peak 21(19p13 2) | 97 (17%) | 478 | 0.144 (1.00) | 0.493 (1.00) | 0.216 (1.00) | 0.182 (1.00) | 0.0503 (1.00) | 0.407 (1.00) | 0.0341 (1.00) | 0.233 (1.00) | 0.125 (1.00) | 1 (1.00)
Amp Peak 22(19q12) | 122 (21%) | 453 | 0.628 (1.00) | 0.941 (1.00) | 0.256 (1.00) | 0.185 (1.00) | 0.0289 (1.00) | 0.662 (1.00) | 0.0969 (1.00) | 0.139 (1.00) | 0.228 (1.00) | 0.692 (1.00)
Amp Peak 23(20p11 23) | 301 (52%) | 274 | 0.699 (1.00) | 0.921 (1.00) | 0.0194 (1.00) | 0.0364 (1.00) | 0.000706 (0.485) | 0.881 (1.00) | 0.0369 (1.00) | 0.00134 (0.901) | 0.0111 (1.00) | 0.181 (1.00)
Amp Peak 28(Xq28) | 121 (21%) | 454 | 0.245 (1.00) | 0.209 (1.00) | 0.421 (1.00) | 0.838 (1.00) | 0.0243 (1.00) | 0.528 (1.00) | 0.0168 (1.00) | 0.219 (1.00) | 0.0632 (1.00) | 0.693 (1.00)
Del Peak 1(1p36 11) | 222 (39%) | 353 | 0.051 (1.00) | 0.105 (1.00) | 0.126 (1.00) | 0.392 (1.00) | 0.00635 (1.00) | 0.238 (1.00) | 0.00091 (0.622) | 0.000615 (0.425) | 0.000727 (0.498) | 0.739 (1.00)
Del Peak 2(1p33) | 156 (27%) | 419 | 0.0178 (1.00) | 0.836 (1.00) | 0.401 (1.00) | 0.851 (1.00) | 0.0793 (1.00) | 0.226 (1.00) | 0.00497 (1.00) | 0.0106 (1.00) | 0.0156 (1.00) | 0.709 (1.00)
Del Peak 3(1p13 2) | 157 (27%) | 418 | 0.0696 (1.00) | 0.841 (1.00) | 0.248 (1.00) | 0.639 (1.00) | 0.135 (1.00) | 0.15 (1.00) | 0.00208 (1.00) | 0.00127 (0.86) | 0.0161 (1.00) | 0.265 (1.00)
Del Peak 4(2p12) | 20 (3%) | 555 | 0.796 (1.00) | 0.179 (1.00) | 0.00346 (1.00) | 0.821 (1.00) | 0.021 (1.00) | 1 (1.00) | 0.358 (1.00) | 0.56 (1.00) | 0.319 (1.00) | 0.275 (1.00)
Del Peak 5(2q22 1) | 33 (6%) | 542 | 0.85 (1.00) | 0.564 (1.00) | 0.842 (1.00) | 0.474 (1.00) | 0.93 (1.00) | 0.683 (1.00) | 0.622 (1.00) | 0.689 (1.00) | 0.172 (1.00) | 1 (1.00)
Del Peak 6(2q37 2) | 30 (5%) | 545 | 0.842 (1.00) | 0.139 (1.00) | 0.835 (1.00) | 0.458 (1.00) | 0.937 (1.00) | 0.343 (1.00) | 0.207 (1.00) | 0.133 (1.00) | 0.0403 (1.00) | 1 (1.00)
Del Peak 7(3p26 3) | 84 (15%) | 491 | 0.000643 (0.443) | 0.855 (1.00) | 0.691 (1.00) | 0.723 (1.00) | 0.191 (1.00) | 0.0365 (1.00) | 0.0192 (1.00) | 0.00105 (0.712) | 0.000658 (0.453) | 0.131 (1.00)
Del Peak 8(3p14 2) | 104 (18%) | 471 | 0.216 (1.00) | 0.578 (1.00) | 0.808 (1.00) | 0.664 (1.00) | 0.417 (1.00) | 0.134 (1.00) | 0.185 (1.00) | 0.0317 (1.00) | 0.0454 (1.00) | 0.669 (1.00)
Del Peak 9(3q26 31) | 56 (10%) | 519 | 0.714 (1.00) | 0.996 (1.00) | 0.874 (1.00) | 0.0931 (1.00) | 0.0407 (1.00) | 0.0132 (1.00) | 0.366 (1.00) | 0.327 (1.00) | 0.00201 (1.00) | 0.216 (1.00)
Del Peak 11(4q22 1) | 198 (34%) | 377 | 0.193 (1.00) | 0.42 (1.00) | 0.00417 (1.00) | 0.187 (1.00) | 0.00139 (0.931) | 0.134 (1.00) | 0.00178 (1.00) | 0.369 (1.00) | 0.0375 (1.00) | 0.00114 (0.771)
Del Peak 12(4q35 1) | 211 (37%) | 364 | 0.277 (1.00) | 0.303 (1.00) | 0.0325 (1.00) | 0.863 (1.00) | 0.0209 (1.00) | 0.708 (1.00) | 0.00331 (1.00) | 0.645 (1.00) | 0.118 (1.00) | 0.00185 (1.00)
Del Peak 13(5q11 2) | 140 (24%) | 435 | 0.164 (1.00) | 0.0866 (1.00) | 0.0389 (1.00) | 1 (1.00) | 0.0272 (1.00) | 0.979 (1.00) | 0.00769 (1.00) | 0.0232 (1.00) | 0.0341 (1.00) | 0.00103 (0.701)
Del Peak 14(5q22 2) | 172 (30%) | 403 | 0.0866 (1.00) | 0.359 (1.00) | 0.155 (1.00) | 0.648 (1.00) | 0.0619 (1.00) | 0.782 (1.00) | 0.0166 (1.00) | 0.0311 (1.00) | 0.033 (1.00) | 0.000382 (0.266)
Del Peak 15(6p25 3) | 78 (14%) | 497 | 0.611 (1.00) | 0.0683 (1.00) | 1 (1.00) | 0.0876 (1.00) | 0.539 (1.00) | 0.256 (1.00) | 0.551 (1.00) | 0.326 (1.00) | 0.22 (1.00) | 0.351 (1.00)
Del Peak 16(6q26) | 90 (16%) | 485 | 0.029 (1.00) | 0.9 (1.00) | 0.368 (1.00) | 0.301 (1.00) | 0.0484 (1.00) | 0.0565 (1.00) | 0.0142 (1.00) | 0.0389 (1.00) | 0.594 (1.00) | 0.637 (1.00)
Del Peak 17(7q31 1) | 15 (3%) | 560 | 1 (1.00) | 0.329 (1.00) | 1 (1.00) | 0.307 (1.00) | 0.503 (1.00) | 0.525 (1.00) | 0.673 (1.00) | 0.33 (1.00) | 0.348 (1.00) | 1 (1.00)
Del Peak 20(8p11 21) | 124 (22%) | 451 | 0.598 (1.00) | 0.329 (1.00) | 0.031 (1.00) | 0.542 (1.00) | 0.164 (1.00) | 0.539 (1.00) | 0.00719 (1.00) | 0.0823 (1.00) | 0.027 (1.00) | 0.414 (1.00)
Del Peak 21(8q11 1) | 44 (8%) | 531 | 0.889 (1.00) | 0.382 (1.00) | 0.16 (1.00) | 0.208 (1.00) | 0.42 (1.00) | 0.722 (1.00) | 0.0273 (1.00) | 0.00202 (1.00) | 0.0949 (1.00) | 0.514 (1.00)
Del Peak 22(9p24 2) | 78 (14%) | 497 | 0.00207 (1.00) | 0.12 (1.00) | 0.496 (1.00) | 0.0507 (1.00) | 0.46 (1.00) | 0.495 (1.00) | 0.135 (1.00) | 0.0231 (1.00) | 0.289 (1.00) | 0.351 (1.00)
Del Peak 23(10p15 3) | 102 (18%) | 473 | 0.577 (1.00) | 0.0282 (1.00) | 0.271 (1.00) | 0.913 (1.00) | 0.364 (1.00) | 0.73 (1.00) | 0.00724 (1.00) | 0.181 (1.00) | 0.00827 (1.00) | 0.00145 (0.967)
Del Peak 24(10q21 1) | 118 (21%) | 457 | 0.869 (1.00) | 0.0152 (1.00) | 0.421 (1.00) | 0.535 (1.00) | 0.116 (1.00) | 0.73 (1.00) | 0.161 (1.00) | 0.682 (1.00) | 0.366 (1.00) | 0.00326 (1.00)
Del Peak 25(10q23 31) | 145 (25%) | 430 | 0.566 (1.00) | 0.00668 (1.00) | 0.0408 (1.00) | 0.923 (1.00) | 0.0202 (1.00) | 0.207 (1.00) | 0.0137 (1.00) | 0.0621 (1.00) | 0.0973 (1.00) | 0.0013 (0.874)
Del Peak 26(10q25 2) | 140 (24%) | 435 | 0.756 (1.00) | 0.0715 (1.00) | 0.128 (1.00) | 0.846 (1.00) | 0.0321 (1.00) | 0.219 (1.00) | 0.0136 (1.00) | 0.43 (1.00) | 0.115 (1.00) | 0.00103 (0.701)
Del Peak 27(11q22 3) | 104 (18%) | 471 | 0.473 (1.00) | 0.396 (1.00) | 0.086 (1.00) | 0.588 (1.00) | 0.0526 (1.00) | 0.391 (1.00) | 0.0515 (1.00) | 0.633 (1.00) | 0.092 (1.00) | 0.061 (1.00)
Del Peak 28(12p13 1) | 77 (13%) | 498 | 0.466 (1.00) | 0.472 (1.00) | 0.0256 (1.00) | 0.327 (1.00) | 0.0006 (0.415) | 0.51 (1.00) | 0.0317 (1.00) | 0.1 (1.00) | 0.206 (1.00) | 0.344 (1.00)
Del Peak 29(12q21 2) | 80 (14%) | 495 | 0.636 (1.00) | 0.709 (1.00) | 0.0779 (1.00) | 0.717 (1.00) | 0.00778 (1.00) | 0.682 (1.00) | 0.0194 (1.00) | 0.0916 (1.00) | 0.239 (1.00) | 0.117 (1.00)
Del Peak 31(15q11 2) | 233 (41%) | 342 | 0.771 (1.00) | 0.618 (1.00) | 0.216 (1.00) | 0.496 (1.00) | 0.0545 (1.00) | 0.809 (1.00) | 0.015 (1.00) | 0.264 (1.00) | 0.0412 (1.00) | 0.035 (1.00)
Del Peak 32(15q21 1) | 227 (39%) | 348 | 0.434 (1.00) | 0.603 (1.00) | 0.0355 (1.00) | 0.305 (1.00) | 0.0246 (1.00) | 0.852 (1.00) | 0.0274 (1.00) | 0.228 (1.00) | 0.125 (1.00) | 0.0327 (1.00)
Del Peak 33(15q22 33) | 217 (38%) | 358 | 0.555 (1.00) | 0.327 (1.00) | 0.012 (1.00) | 0.667 (1.00) | 0.00584 (1.00) | 0.0961 (1.00) | 0.00685 (1.00) | 0.211 (1.00) | 0.0233 (1.00) | 0.00229 (1.00)
Del Peak 35(16q23 1) | 72 (13%) | 503 | 0.0014 (0.934) | 0.264 (1.00) | 0.402 (1.00) | 0.167 (1.00) | 0.513 (1.00) | 0.251 (1.00) | 0.76 (1.00) | 0.951 (1.00) | 0.469 (1.00) | 1 (1.00)
Del Peak 37(17q24 3) | 84 (15%) | 491 | 0.731 (1.00) | 0.305 (1.00) | 0.793 (1.00) | 0.0994 (1.00) | 0.995 (1.00) | 0.234 (1.00) | 0.0072 (1.00) | 0.352 (1.00) | 0.0348 (1.00) | 0.626 (1.00)
Del Peak 43(19q13 43) | 68 (12%) | 507 | 0.509 (1.00) | 0.816 (1.00) | 0.146 (1.00) | 0.3 (1.00) | 0.416 (1.00) | 0.438 (1.00) | 0.0155 (1.00) | 0.0712 (1.00) | 0.167 (1.00) | 0.289 (1.00)
Del Peak 44(20p12 1) | 179 (31%) | 396 | 0.108 (1.00) | 0.631 (1.00) | 0.0445 (1.00) | 0.321 (1.00) | 0.142 (1.00) | 0.47 (1.00) | 0.317 (1.00) | 0.827 (1.00) | 0.192 (1.00) | 0.0632 (1.00)
Del Peak 45(20p12 1) | 179 (31%) | 396 | 0.108 (1.00) | 0.631 (1.00) | 0.0445 (1.00) | 0.321 (1.00) | 0.142 (1.00) | 0.47 (1.00) | 0.317 (1.00) | 0.827 (1.00) | 0.192 (1.00) | 0.0632 (1.00)
Del Peak 46(21q11 2) | 195 (34%) | 380 | 0.515 (1.00) | 0.721 (1.00) | 0.00555 (1.00) | 0.66 (1.00) | 0.000615 (0.425) | 0.824 (1.00) | 0.0459 (1.00) | 0.614 (1.00) | 0.326 (1.00) | 0.175 (1.00)
Del Peak 47(22q13 32) | 204 (35%) | 371 | 0.04 (1.00) | 0.672 (1.00) | 0.173 (1.00) | 0.93 (1.00) | 0.0094 (1.00) | 0.445 (1.00) | 0.000796 (0.545) | 0.0275 (1.00) | 0.00928 (1.00) | 0.727 (1.00)

'Amp Peak 5(6p21.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 3.15e-05 (Fisher's exact test), Q value = 0.023

Table S1. Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
AMP PEAK 5(6P21.1) MUTATED | 63 | 39 | 43
AMP PEAK 5(6P21.1) WILD-TYPE | 265 | 101 | 60

Figure S1. Get High-res Image Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 5(6p21.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000322 (Fisher's exact test), Q value = 0.23

Table S2. Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
AMP PEAK 5(6P21.1) MUTATED | 18 | 38 | 55 | 30
AMP PEAK 5(6P21.1) WILD-TYPE | 79 | 169 | 111 | 51

Figure S2. Get High-res Image Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 6(7p21.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000219 (Fisher's exact test), Q value = 0.15

Table S3. Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
AMP PEAK 6(7P21.3) MUTATED | 210 | 20 | 99 | 5
AMP PEAK 6(7P21.3) WILD-TYPE | 146 | 34 | 44 | 8

Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 6(7p21.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 1.22e-05 (Fisher's exact test), Q value = 0.0088

Table S4. Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
AMP PEAK 6(7P21.3) MUTATED | 164 | 100 | 69
AMP PEAK 6(7P21.3) WILD-TYPE | 164 | 40 | 34

Figure S4. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 6(7p21.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.31e-06 (Fisher's exact test), Q value = 0.0031

Table S5. Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
AMP PEAK 6(7P21.3) MUTATED | 54 | 93 | 114 | 57
AMP PEAK 6(7P21.3) WILD-TYPE | 43 | 114 | 52 | 24

Figure S5. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 14(13q12.13) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-09 (Fisher's exact test), Q value = 7.7e-07

Table S6. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
AMP PEAK 14(13Q12.13) MUTATED | 233 | 16 | 112 | 5
AMP PEAK 14(13Q12.13) WILD-TYPE | 123 | 38 | 31 | 8

Figure S6. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 14(13q12.13) mutation analysis' versus 'PATHOLOGY.N'

P value = 3.94e-05 (Fisher's exact test), Q value = 0.028

Table S7. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
AMP PEAK 14(13Q12.13) MUTATED | 186 | 105 | 77
AMP PEAK 14(13Q12.13) WILD-TYPE | 142 | 35 | 26

Figure S7. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 14(13q12.13) mutation analysis' versus 'TUMOR.STAGE'

P value = 7.37e-05 (Fisher's exact test), Q value = 0.052

Table S8. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
AMP PEAK 14(13Q12.13) MUTATED | 60 | 112 | 117 | 65
AMP PEAK 14(13Q12.13) WILD-TYPE | 37 | 95 | 49 | 16

Figure S8. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 15(13q12.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.33e-09 (Fisher's exact test), Q value = 1.7e-06

Table S9. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
AMP PEAK 15(13Q12.2) MUTATED | 229 | 16 | 111 | 5
AMP PEAK 15(13Q12.2) WILD-TYPE | 127 | 38 | 32 | 8

Figure S9. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 15(13q12.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 9.29e-05 (Fisher's exact test), Q value = 0.066

Table S10. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
AMP PEAK 15(13Q12.2) MUTATED | 184 | 103 | 76
AMP PEAK 15(13Q12.2) WILD-TYPE | 144 | 37 | 27

Figure S10. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 15(13q12.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000181 (Fisher's exact test), Q value = 0.13

Table S11. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
AMP PEAK 15(13Q12.2) MUTATED | 60 | 110 | 116 | 63
AMP PEAK 15(13Q12.2) WILD-TYPE | 37 | 97 | 50 | 18

Figure S11. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 16(13q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.84e-08 (Fisher's exact test), Q value = 2.1e-05

Table S12. Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
AMP PEAK 16(13Q22.1) MUTATED | 235 | 18 | 109 | 4
AMP PEAK 16(13Q22.1) WILD-TYPE | 121 | 36 | 34 | 9

Figure S12. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 16(13q22.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000126 (Fisher's exact test), Q value = 0.089

Table S13. Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
AMP PEAK 16(13Q22.1) MUTATED | 187 | 105 | 75
AMP PEAK 16(13Q22.1) WILD-TYPE | 141 | 35 | 28

Figure S13. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 18(16p11.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 5.86e-05 (Fisher's exact test), Q value = 0.042

Table S14. Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
AMP PEAK 18(16P11.2) MUTATED | 68 | 52 | 39
AMP PEAK 18(16P11.2) WILD-TYPE | 260 | 88 | 64

Figure S14. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 18(16p11.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 8.31e-05 (Fisher's exact test), Q value = 0.059

Table S15. Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
AMP PEAK 18(16P11.2) MUTATED | 19 | 40 | 64 | 27
AMP PEAK 18(16P11.2) WILD-TYPE | 78 | 167 | 102 | 54

Figure S15. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 24(20p11.21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0078

Table S16. Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
AMP PEAK 24(20P11.21) MUTATED | 207 | 20 | 103 | 4
AMP PEAK 24(20P11.21) WILD-TYPE | 149 | 34 | 40 | 9

Figure S16. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 25(20q11.21) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.13e-06 (Fisher's exact test), Q value = 0.0066

Table S17. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 412 | 159
AMP PEAK 25(20Q11.21) MUTATED | 295 | 141
AMP PEAK 25(20Q11.21) WILD-TYPE | 117 | 18

Figure S17. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 25(20q11.21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.89e-12 (Fisher's exact test), Q value = 4.4e-09

Table S18. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
AMP PEAK 25(20Q11.21) MUTATED | 269 | 24 | 132 | 7
AMP PEAK 25(20Q11.21) WILD-TYPE | 87 | 30 | 11 | 6

Figure S18. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 25(20q11.21) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000105 (Fisher's exact test), Q value = 0.074

Table S19. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
AMP PEAK 25(20Q11.21) MUTATED | 74 | 136 | 136 | 71
AMP PEAK 25(20Q11.21) WILD-TYPE | 23 | 71 | 30 | 10

Figure S19. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 26(20q12) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.74e-06 (Fisher's exact test), Q value = 0.0034

Table S20. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 412 | 159
AMP PEAK 26(20Q12) MUTATED | 296 | 142
AMP PEAK 26(20Q12) WILD-TYPE | 116 | 17

Figure S20. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 26(20q12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.83e-13 (Fisher's exact test), Q value = 2.9e-10

Table S21. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
AMP PEAK 26(20Q12) MUTATED | 271 | 23 | 133 | 7
AMP PEAK 26(20Q12) WILD-TYPE | 85 | 31 | 10 | 6

Figure S21. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 26(20q12) mutation analysis' versus 'TUMOR.STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S22. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
AMP PEAK 26(20Q12) MUTATED | 74 | 137 | 135 | 73
AMP PEAK 26(20Q12) WILD-TYPE | 23 | 70 | 31 | 8

Figure S22. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 27(20q13.32) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.016

Table S23. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 412 | 159
AMP PEAK 27(20Q13.32) MUTATED | 299 | 141
AMP PEAK 27(20Q13.32) WILD-TYPE | 113 | 18

Figure S23. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 27(20q13.32) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.45e-12 (Fisher's exact test), Q value = 4.8e-09

Table S24. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
AMP PEAK 27(20Q13.32) MUTATED | 273 | 24 | 132 | 7
AMP PEAK 27(20Q13.32) WILD-TYPE | 83 | 30 | 11 | 6

Figure S24. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 27(20q13.32) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000128 (Fisher's exact test), Q value = 0.09

Table S25. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
AMP PEAK 27(20Q13.32) MUTATED | 74 | 139 | 137 | 72
AMP PEAK 27(20Q13.32) WILD-TYPE | 23 | 68 | 29 | 9

Figure S25. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 10(4p16.1) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.02

Table S26. Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 566 | 9
DEL PEAK 10(4P16.1) MUTATED | 173 | 9
DEL PEAK 10(4P16.1) WILD-TYPE | 393 | 0

Figure S26. Get High-res Image Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 18(8p23.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.4e-05 (Fisher's exact test), Q value = 0.017

Table S27. Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 412 | 159
DEL PEAK 18(8P23.2) MUTATED | 172 | 98
DEL PEAK 18(8P23.2) WILD-TYPE | 240 | 61

Figure S27. Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 18(8p23.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.8e-05 (Fisher's exact test), Q value = 0.02

Table S28. Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
DEL PEAK 18(8P23.2) MUTATED | 156 | 15 | 89 | 7
DEL PEAK 18(8P23.2) WILD-TYPE | 200 | 39 | 54 | 6

Figure S28. Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 18(8p23.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.02

Table S29. Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
DEL PEAK 18(8P23.2) MUTATED | 129 | 75 | 65
DEL PEAK 18(8P23.2) WILD-TYPE | 199 | 65 | 38

Figure S29. Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 18(8p23.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.024

Table S30. Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
DEL PEAK 18(8P23.2) MUTATED | 39 | 78 | 92 | 52
DEL PEAK 18(8P23.2) WILD-TYPE | 58 | 129 | 74 | 29

Figure S30. Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 19(8p22) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000248 (Fisher's exact test), Q value = 0.17

Table S31. Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
DEL PEAK 19(8P22) MUTATED | 168 | 16 | 89 | 7
DEL PEAK 19(8P22) WILD-TYPE | 188 | 38 | 54 | 6

Figure S31. Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

P value = 1.96e-06 (Fisher's exact test), Q value = 0.0014

Table S32. Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
DEL PEAK 19(8P22) MUTATED | 134 | 78 | 70
DEL PEAK 19(8P22) WILD-TYPE | 194 | 62 | 33

Figure S32. Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

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

P value = 1.22e-06 (Fisher's exact test), Q value = 9e-04

Table S33. Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
DEL PEAK 19(8P22) MUTATED | 39 | 81 | 99 | 55
DEL PEAK 19(8P22) WILD-TYPE | 58 | 126 | 67 | 26

Figure S33. Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 30(14q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.08e-06 (Fisher's exact test), Q value = 8e-04

Table S34. Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
DEL PEAK 30(14Q22.1) MUTATED | 115 | 4 | 62 | 1
DEL PEAK 30(14Q22.1) WILD-TYPE | 241 | 50 | 81 | 12

Figure S34. Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 34(16p13.3) mutation analysis' versus 'Time to Death'

P value = 4.34e-05 (logrank test), Q value = 0.031

Table S35. Gene #62: 'Del Peak 34(16p13.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 444 | 60 | 0.1 - 135.5 (7.0)
DEL PEAK 34(16P13.3) MUTATED | 42 | 13 | 0.2 - 49.9 (7.6)
DEL PEAK 34(16P13.3) WILD-TYPE | 402 | 47 | 0.1 - 135.5 (7.0)

Figure S35. Get High-res Image Gene #62: 'Del Peak 34(16p13.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 36(17p12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.98e-08 (Fisher's exact test), Q value = 4.4e-05

Table S36. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
DEL PEAK 36(17P12) MUTATED | 213 | 14 | 103 | 6
DEL PEAK 36(17P12) WILD-TYPE | 143 | 40 | 40 | 7

Figure S36. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 36(17p12) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000119 (Fisher's exact test), Q value = 0.084

Table S37. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
DEL PEAK 36(17P12) MUTATED | 171 | 95 | 74
DEL PEAK 36(17P12) WILD-TYPE | 157 | 45 | 29

Figure S37. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 36(17p12) mutation analysis' versus 'TUMOR.STAGE'

P value = 3.09e-05 (Fisher's exact test), Q value = 0.022

Table S38. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
DEL PEAK 36(17P12) MUTATED | 50 | 104 | 116 | 59
DEL PEAK 36(17P12) WILD-TYPE | 47 | 103 | 50 | 22

Figure S38. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 38(18p11.31) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.82e-06 (Fisher's exact test), Q value = 0.0013

Table S39. Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 412 | 159
DEL PEAK 38(18P11.31) MUTATED | 219 | 119
DEL PEAK 38(18P11.31) WILD-TYPE | 193 | 40

Figure S39. Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 38(18p11.31) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.11e-16 (Fisher's exact test), Q value = 8.3e-14

Table S40. Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
DEL PEAK 38(18P11.31) MUTATED | 211 | 7 | 113 | 6
DEL PEAK 38(18P11.31) WILD-TYPE | 145 | 47 | 30 | 7

Figure S40. Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 39(18q12.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.57e-09 (Fisher's exact test), Q value = 1.2e-06

Table S41. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 412 | 159
DEL PEAK 39(18Q12.2) MUTATED | 247 | 136
DEL PEAK 39(18Q12.2) WILD-TYPE | 165 | 23

Figure S41. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 39(18q12.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.64e-18 (Fisher's exact test), Q value = 4.2e-15

Table S42. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
DEL PEAK 39(18Q12.2) MUTATED | 235 | 11 | 125 | 10
DEL PEAK 39(18Q12.2) WILD-TYPE | 121 | 43 | 18 | 3

Figure S42. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 39(18q12.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000131 (Fisher's exact test), Q value = 0.092

Table S43. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
DEL PEAK 39(18Q12.2) MUTATED | 196 | 107 | 79
DEL PEAK 39(18Q12.2) WILD-TYPE | 132 | 33 | 24

Figure S43. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 39(18q12.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 6.7e-05 (Fisher's exact test), Q value = 0.048

Table S44. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
DEL PEAK 39(18Q12.2) MUTATED | 56 | 122 | 121 | 67
DEL PEAK 39(18Q12.2) WILD-TYPE | 41 | 85 | 45 | 14

Figure S44. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 40(18q21.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.07e-09 (Fisher's exact test), Q value = 7.9e-07

Table S45. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 412 | 159
DEL PEAK 40(18Q21.2) MUTATED | 260 | 140
DEL PEAK 40(18Q21.2) WILD-TYPE | 152 | 19

Figure S45. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 40(18q21.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.57e-16 (Fisher's exact test), Q value = 1.9e-13

Table S46. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
DEL PEAK 40(18Q21.2) MUTATED | 245 | 14 | 126 | 12
DEL PEAK 40(18Q21.2) WILD-TYPE | 111 | 40 | 17 | 1

Figure S46. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 40(18q21.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 2.01e-06 (Fisher's exact test), Q value = 0.0015

Table S47. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
DEL PEAK 40(18Q21.2) MUTATED | 202 | 111 | 86
DEL PEAK 40(18Q21.2) WILD-TYPE | 126 | 29 | 17

Figure S47. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 40(18q21.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 3.94e-07 (Fisher's exact test), Q value = 0.00029

Table S48. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
DEL PEAK 40(18Q21.2) MUTATED | 58 | 126 | 128 | 72
DEL PEAK 40(18Q21.2) WILD-TYPE | 39 | 81 | 38 | 9

Figure S48. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 41(18q22.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.94e-07 (Fisher's exact test), Q value = 0.00014

Table S49. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | COLON | RECTUM
--- | --- | ---
ALL | 412 | 159
DEL PEAK 41(18Q22.1) MUTATED | 260 | 135
DEL PEAK 41(18Q22.1) WILD-TYPE | 152 | 24

Figure S49. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 41(18q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.41e-15 (Fisher's exact test), Q value = 1.1e-12

Table S50. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA
--- | --- | --- | --- | ---
ALL | 356 | 54 | 143 | 13
DEL PEAK 41(18Q22.1) MUTATED | 246 | 13 | 124 | 10
DEL PEAK 41(18Q22.1) WILD-TYPE | 110 | 41 | 19 | 3

Figure S50. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 41(18q22.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.008

Table S51. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
DEL PEAK 41(18Q22.1) MUTATED | 201 | 108 | 85
DEL PEAK 41(18Q22.1) WILD-TYPE | 127 | 32 | 18

Figure S51. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 41(18q22.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.52e-06 (Fisher's exact test), Q value = 0.0033

Table S52. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 97 | 207 | 166 | 81
DEL PEAK 41(18Q22.1) MUTATED | 58 | 126 | 124 | 71
DEL PEAK 41(18Q22.1) WILD-TYPE | 39 | 81 | 42 | 10

Figure S52. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 42(19p13.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 7.59e-05 (Fisher's exact test), Q value = 0.054

Table S53. Gene #70: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2
--- | --- | --- | ---
ALL | 328 | 140 | 103
DEL PEAK 42(19P13.3) MUTATED | 36 | 26 | 30
DEL PEAK 42(19P13.3) WILD-TYPE | 292 | 114 | 73

Figure S53. Get High-res Image Gene #70: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

Methods & Data
Input

- Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

- Clinical data file = COADREAD-TP.clin.merged.picked.txt

- Number of patients = 575

- Number of copy number variation regions = 75

- Number of selected clinical features = 10

- Exclude regions that fewer than K tumors have alterations, K = 3

Survival analysis

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

Student's t-test analysis

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

Fisher's exact test

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

Chi-square test

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

Q value calculation

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

Download Results

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

- 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)
[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)
[6] GISTIC_version2
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