This pipeline computes the correlation between significant copy number variation (cnv) genes and selected clinical features.
Testing the association between copy number variation of 68 peak regions and 9 clinical features across 413 patients, 35 significant findings detected with Q value < 0.25.
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Amp Peak 11(13q12.13) cnvs correlated to 'HISTOLOGICAL.TYPE'.
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Amp Peak 12(13q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.
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Amp Peak 13(16p11.2) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
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Amp Peak 14(16q12.1) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
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Amp Peak 22(20q11.21) cnvs correlated to 'HISTOLOGICAL.TYPE'.
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Amp Peak 23(20q12) cnvs correlated to 'HISTOLOGICAL.TYPE'.
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Amp Peak 24(20q13.32) cnvs correlated to 'HISTOLOGICAL.TYPE'.
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Del Peak 1(1p36.11) cnvs correlated to 'PATHOLOGICSPREAD(M)'.
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Del Peak 6(3p26.1) cnvs correlated to 'Time to Death'.
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Del Peak 9(4p16.2) cnvs correlated to 'Time to Death', 'PATHOLOGY.N', and 'PATHOLOGICSPREAD(M)'.
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Del Peak 13(5q21.3) cnvs correlated to 'PATHOLOGY.N'.
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Del Peak 18(8p23.3) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
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Del Peak 19(8p22) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
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Del Peak 21(8p11.21) cnvs correlated to 'PATHOLOGY.N'.
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Del Peak 28(13q14.13) cnvs correlated to 'PATHOLOGICSPREAD(M)'.
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Del Peak 35(17p12) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Del Peak 37(18p11.31) cnvs correlated to 'HISTOLOGICAL.TYPE'.
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Del Peak 38(18q12.2) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.
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Del Peak 39(18q21.2) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Del Peak 40(18q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Del Peak 41(19p13.3) cnvs correlated to 'PATHOLOGY.N'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 68 regions 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 |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | |
Del Peak 9(4p16 2) | 121 (29%) | 292 |
0.00024 (0.141) |
0.609 (1.00) |
0.59 (1.00) |
0.036 (1.00) |
0.671 (1.00) |
0.000257 (0.15) |
0.000266 (0.155) |
0.000571 (0.326) |
0.0247 (1.00) |
Del Peak 35(17p12) | 229 (55%) | 184 |
0.334 (1.00) |
0.0108 (1.00) |
0.43 (1.00) |
3.38e-06 (0.00204) |
0.868 (1.00) |
2.62e-05 (0.0157) |
0.0165 (1.00) |
1.15e-06 (0.000694) |
0.257 (1.00) |
Del Peak 39(18q21 2) | 260 (63%) | 153 |
0.4 (1.00) |
0.0992 (1.00) |
0.127 (1.00) |
3.87e-09 (2.35e-06) |
0.813 (1.00) |
0.000105 (0.0622) |
0.00624 (1.00) |
8.87e-06 (0.00531) |
0.299 (1.00) |
Del Peak 40(18q22 1) | 260 (63%) | 153 |
0.263 (1.00) |
0.176 (1.00) |
0.127 (1.00) |
4.48e-10 (2.73e-07) |
0.813 (1.00) |
0.000105 (0.0622) |
0.00624 (1.00) |
1.94e-05 (0.0116) |
0.299 (1.00) |
Amp Peak 12(13q22 1) | 254 (62%) | 159 |
0.0716 (1.00) |
0.565 (1.00) |
0.363 (1.00) |
8.13e-06 (0.00488) |
1 (1.00) |
0.00146 (0.814) |
0.00698 (1.00) |
0.000308 (0.179) |
0.288 (1.00) |
Amp Peak 13(16p11 2) | 116 (28%) | 297 |
0.426 (1.00) |
0.0688 (1.00) |
0.584 (1.00) |
0.00867 (1.00) |
0.479 (1.00) |
0.000133 (0.0782) |
0.323 (1.00) |
0.000155 (0.0912) |
1 (1.00) |
Amp Peak 14(16q12 1) | 102 (25%) | 311 |
0.356 (1.00) |
0.0166 (1.00) |
0.493 (1.00) |
0.0112 (1.00) |
0.951 (1.00) |
0.000188 (0.11) |
0.18 (1.00) |
2.82e-05 (0.0168) |
0.574 (1.00) |
Del Peak 18(8p23 3) | 171 (41%) | 242 |
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) |
9.03e-05 (0.0535) |
0.572 (1.00) |
Del Peak 19(8p22) | 185 (45%) | 228 |
0.433 (1.00) |
0.104 (1.00) |
0.321 (1.00) |
0.0185 (1.00) |
0.223 (1.00) |
8.04e-06 (0.00483) |
0.00136 (0.763) |
2.07e-07 (0.000126) |
0.589 (1.00) |
Del Peak 38(18q12 2) | 247 (60%) | 166 |
0.983 (1.00) |
0.0542 (1.00) |
0.421 (1.00) |
3.02e-10 (1.84e-07) |
0.84 (1.00) |
0.00201 (1.00) |
0.0125 (1.00) |
0.000369 (0.214) |
0.277 (1.00) |
Amp Peak 11(13q12 13) | 250 (61%) | 163 |
0.29 (1.00) |
0.522 (1.00) |
0.92 (1.00) |
8.87e-07 (0.000538) |
0.972 (1.00) |
0.00316 (1.00) |
0.00471 (1.00) |
0.000458 (0.264) |
0.282 (1.00) |
Amp Peak 22(20q11 21) | 296 (72%) | 117 |
0.433 (1.00) |
0.474 (1.00) |
0.382 (1.00) |
7.66e-06 (0.00461) |
0.541 (1.00) |
0.0241 (1.00) |
0.0102 (1.00) |
0.000849 (0.483) |
0.562 (1.00) |
Amp Peak 23(20q12) | 297 (72%) | 116 |
0.365 (1.00) |
0.51 (1.00) |
0.324 (1.00) |
1.38e-06 (0.000832) |
0.676 (1.00) |
0.0286 (1.00) |
0.00474 (1.00) |
0.00057 (0.326) |
0.563 (1.00) |
Amp Peak 24(20q13 32) | 300 (73%) | 113 |
0.371 (1.00) |
0.537 (1.00) |
0.377 (1.00) |
4.8e-06 (0.00289) |
0.641 (1.00) |
0.0179 (1.00) |
0.00667 (1.00) |
0.000552 (0.317) |
0.565 (1.00) |
Del Peak 1(1p36 11) | 150 (36%) | 263 |
0.0209 (1.00) |
0.144 (1.00) |
0.54 (1.00) |
0.00362 (1.00) |
0.66 (1.00) |
0.00492 (1.00) |
0.000122 (0.0717) |
0.000869 (0.493) |
1 (1.00) |
Del Peak 6(3p26 1) | 60 (15%) | 353 |
0.000411 (0.238) |
0.346 (1.00) |
1 (1.00) |
0.146 (1.00) |
0.0576 (1.00) |
0.0189 (1.00) |
0.000457 (0.264) |
0.000506 (0.291) |
1 (1.00) |
Del Peak 13(5q21 3) | 117 (28%) | 296 |
0.0728 (1.00) |
0.0679 (1.00) |
0.743 (1.00) |
0.196 (1.00) |
0.983 (1.00) |
5.21e-05 (0.0309) |
0.0201 (1.00) |
0.000559 (0.32) |
0.0223 (1.00) |
Del Peak 21(8p11 21) | 43 (10%) | 370 |
0.826 (1.00) |
0.377 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.155 (1.00) |
0.000288 (0.168) |
0.00793 (1.00) |
0.000868 (0.493) |
0.282 (1.00) |
Del Peak 28(13q14 13) | 18 (4%) | 395 |
0.312 (1.00) |
0.279 (1.00) |
1 (1.00) |
1 (1.00) |
0.719 (1.00) |
0.0646 (1.00) |
4.33e-05 (0.0258) |
0.851 (1.00) |
1 (1.00) |
Del Peak 37(18p11 31) | 220 (53%) | 193 |
0.869 (1.00) |
0.0199 (1.00) |
1 (1.00) |
8.39e-11 (5.13e-08) |
0.822 (1.00) |
0.0483 (1.00) |
0.00385 (1.00) |
0.00179 (0.993) |
0.251 (1.00) |
Del Peak 41(19p13 3) | 57 (14%) | 356 |
0.367 (1.00) |
0.148 (1.00) |
0.67 (1.00) |
0.202 (1.00) |
0.956 (1.00) |
5.5e-05 (0.0326) |
0.0321 (1.00) |
0.00155 (0.866) |
0.36 (1.00) |
Amp Peak 1(2q33 1) | 79 (19%) | 334 |
0.0421 (1.00) |
0.358 (1.00) |
0.259 (1.00) |
0.267 (1.00) |
0.844 (1.00) |
0.0211 (1.00) |
0.639 (1.00) |
0.0496 (1.00) |
0.472 (1.00) |
Amp Peak 2(5p13 2) | 81 (20%) | 332 |
0.344 (1.00) |
0.234 (1.00) |
0.322 (1.00) |
0.856 (1.00) |
0.525 (1.00) |
0.0355 (1.00) |
0.729 (1.00) |
0.782 (1.00) |
1 (1.00) |
Amp Peak 3(5q22 3) | 40 (10%) | 373 |
0.975 (1.00) |
0.768 (1.00) |
0.74 (1.00) |
0.332 (1.00) |
0.787 (1.00) |
0.204 (1.00) |
0.00941 (1.00) |
0.0708 (1.00) |
0.264 (1.00) |
Amp Peak 4(6p21 1) | 89 (22%) | 324 |
0.855 (1.00) |
0.829 (1.00) |
0.283 (1.00) |
0.0505 (1.00) |
0.575 (1.00) |
0.00141 (0.787) |
0.609 (1.00) |
0.0104 (1.00) |
0.00974 (1.00) |
Amp Peak 5(8p11 23) | 144 (35%) | 269 |
0.875 (1.00) |
0.293 (1.00) |
0.757 (1.00) |
0.168 (1.00) |
0.795 (1.00) |
0.744 (1.00) |
0.569 (1.00) |
0.931 (1.00) |
0.279 (1.00) |
Amp Peak 6(8p11 21) | 173 (42%) | 240 |
0.419 (1.00) |
0.449 (1.00) |
0.272 (1.00) |
0.184 (1.00) |
0.762 (1.00) |
0.562 (1.00) |
0.466 (1.00) |
0.962 (1.00) |
0.574 (1.00) |
Amp Peak 7(8q12 1) | 215 (52%) | 198 |
0.858 (1.00) |
0.113 (1.00) |
0.844 (1.00) |
0.0189 (1.00) |
0.421 (1.00) |
0.363 (1.00) |
0.158 (1.00) |
0.395 (1.00) |
0.249 (1.00) |
Amp Peak 8(8q24 21) | 239 (58%) | 174 |
0.637 (1.00) |
0.074 (1.00) |
0.485 (1.00) |
0.0753 (1.00) |
0.2 (1.00) |
0.287 (1.00) |
0.0847 (1.00) |
0.249 (1.00) |
0.267 (1.00) |
Amp Peak 9(11p15 5) | 86 (21%) | 327 |
0.603 (1.00) |
0.0407 (1.00) |
0.544 (1.00) |
0.00194 (1.00) |
0.151 (1.00) |
0.279 (1.00) |
0.254 (1.00) |
0.154 (1.00) |
0.111 (1.00) |
Amp Peak 10(12p13 33) | 104 (25%) | 309 |
0.2 (1.00) |
0.139 (1.00) |
0.734 (1.00) |
0.501 (1.00) |
0.159 (1.00) |
0.14 (1.00) |
0.2 (1.00) |
0.113 (1.00) |
0.575 (1.00) |
Amp Peak 15(17q12) | 101 (24%) | 312 |
0.479 (1.00) |
0.45 (1.00) |
0.252 (1.00) |
0.313 (1.00) |
0.247 (1.00) |
0.113 (1.00) |
0.0126 (1.00) |
0.0169 (1.00) |
0.57 (1.00) |
Amp Peak 16(17q24 1) | 92 (22%) | 321 |
0.076 (1.00) |
0.414 (1.00) |
0.638 (1.00) |
0.112 (1.00) |
0.409 (1.00) |
0.342 (1.00) |
0.0351 (1.00) |
0.209 (1.00) |
0.531 (1.00) |
Amp Peak 17(19p13 2) | 65 (16%) | 348 |
0.63 (1.00) |
0.618 (1.00) |
0.0575 (1.00) |
0.228 (1.00) |
0.669 (1.00) |
0.0189 (1.00) |
0.00672 (1.00) |
0.228 (1.00) |
0.403 (1.00) |
Amp Peak 18(19q13 11) | 83 (20%) | 330 |
0.201 (1.00) |
0.68 (1.00) |
0.0648 (1.00) |
0.364 (1.00) |
0.945 (1.00) |
0.13 (1.00) |
0.0224 (1.00) |
0.489 (1.00) |
0.491 (1.00) |
Amp Peak 19(20p12 3) | 184 (45%) | 229 |
0.0533 (1.00) |
0.491 (1.00) |
0.197 (1.00) |
0.0554 (1.00) |
0.97 (1.00) |
0.0801 (1.00) |
0.00371 (1.00) |
0.00696 (1.00) |
0.0876 (1.00) |
Amp Peak 20(20p11 23) | 205 (50%) | 208 |
0.234 (1.00) |
0.974 (1.00) |
0.2 (1.00) |
0.0127 (1.00) |
0.952 (1.00) |
0.061 (1.00) |
0.00206 (1.00) |
0.00871 (1.00) |
0.121 (1.00) |
Amp Peak 21(20p11 21) | 230 (56%) | 183 |
0.453 (1.00) |
0.466 (1.00) |
0.165 (1.00) |
0.00494 (1.00) |
0.905 (1.00) |
0.276 (1.00) |
0.00305 (1.00) |
0.013 (1.00) |
0.258 (1.00) |
Del Peak 2(1p33) | 107 (26%) | 306 |
0.00122 (0.684) |
0.89 (1.00) |
0.91 (1.00) |
0.132 (1.00) |
0.512 (1.00) |
0.00453 (1.00) |
0.00786 (1.00) |
0.0143 (1.00) |
0.572 (1.00) |
Del Peak 3(1p13 1) | 103 (25%) | 310 |
0.0503 (1.00) |
0.891 (1.00) |
0.496 (1.00) |
0.133 (1.00) |
0.545 (1.00) |
0.00101 (0.567) |
0.000797 (0.454) |
0.00853 (1.00) |
1 (1.00) |
Del Peak 4(1q43) | 44 (11%) | 369 |
0.488 (1.00) |
0.525 (1.00) |
0.875 (1.00) |
0.818 (1.00) |
0.286 (1.00) |
0.181 (1.00) |
0.077 (1.00) |
0.156 (1.00) |
0.287 (1.00) |
Del Peak 5(2q37 2) | 21 (5%) | 392 |
0.368 (1.00) |
0.447 (1.00) |
0.374 (1.00) |
0.748 (1.00) |
0.447 (1.00) |
0.86 (1.00) |
0.361 (1.00) |
0.462 (1.00) |
1 (1.00) |
Del Peak 7(3p14 2) | 75 (18%) | 338 |
0.426 (1.00) |
0.608 (1.00) |
0.371 (1.00) |
0.186 (1.00) |
0.186 (1.00) |
0.0474 (1.00) |
0.0569 (1.00) |
0.0517 (1.00) |
1 (1.00) |
Del Peak 8(3q26 31) | 39 (9%) | 374 |
0.452 (1.00) |
0.85 (1.00) |
1 (1.00) |
0.14 (1.00) |
0.0927 (1.00) |
0.593 (1.00) |
0.619 (1.00) |
0.165 (1.00) |
1 (1.00) |
Del Peak 10(4q22 1) | 126 (31%) | 287 |
0.009 (1.00) |
0.967 (1.00) |
0.593 (1.00) |
0.0174 (1.00) |
0.341 (1.00) |
0.00174 (0.967) |
0.118 (1.00) |
0.0167 (1.00) |
0.0279 (1.00) |
Del Peak 11(4q35 1) | 137 (33%) | 276 |
0.0437 (1.00) |
0.255 (1.00) |
0.249 (1.00) |
0.0871 (1.00) |
0.721 (1.00) |
0.00591 (1.00) |
0.221 (1.00) |
0.042 (1.00) |
0.036 (1.00) |
Del Peak 12(5q11 2) | 91 (22%) | 322 |
0.0477 (1.00) |
0.0453 (1.00) |
0.408 (1.00) |
0.112 (1.00) |
0.901 (1.00) |
0.00305 (1.00) |
0.0574 (1.00) |
0.00873 (1.00) |
0.124 (1.00) |
Del Peak 14(5q23 1) | 107 (26%) | 306 |
0.129 (1.00) |
0.285 (1.00) |
0.311 (1.00) |
0.0983 (1.00) |
0.958 (1.00) |
0.00587 (1.00) |
0.0116 (1.00) |
0.0362 (1.00) |
0.017 (1.00) |
Del Peak 15(6p25 3) | 54 (13%) | 359 |
0.704 (1.00) |
0.0948 (1.00) |
0.0794 (1.00) |
0.516 (1.00) |
0.122 (1.00) |
0.937 (1.00) |
0.18 (1.00) |
0.838 (1.00) |
1 (1.00) |
Del Peak 16(6q26) | 60 (15%) | 353 |
0.0205 (1.00) |
0.928 (1.00) |
0.782 (1.00) |
1 (1.00) |
0.197 (1.00) |
0.0241 (1.00) |
0.0212 (1.00) |
0.111 (1.00) |
1 (1.00) |
Del Peak 17(7q31 1) | 11 (3%) | 402 |
0.978 (1.00) |
0.589 (1.00) |
0.36 (1.00) |
1 (1.00) |
0.571 (1.00) |
1 (1.00) |
0.498 (1.00) |
0.493 (1.00) |
1 (1.00) |
Del Peak 20(8p11 22) | 80 (19%) | 333 |
0.412 (1.00) |
0.236 (1.00) |
0.803 (1.00) |
0.461 (1.00) |
0.344 (1.00) |
0.000878 (0.497) |
0.0887 (1.00) |
0.00256 (1.00) |
0.0973 (1.00) |
Del Peak 22(9p21 3) | 56 (14%) | 357 |
0.0248 (1.00) |
0.0603 (1.00) |
0.251 (1.00) |
0.202 (1.00) |
0.3 (1.00) |
0.147 (1.00) |
0.106 (1.00) |
0.404 (1.00) |
1 (1.00) |
Del Peak 23(10p15 3) | 68 (16%) | 345 |
0.847 (1.00) |
0.434 (1.00) |
0.791 (1.00) |
0.557 (1.00) |
0.852 (1.00) |
0.00165 (0.918) |
0.00231 (1.00) |
0.00103 (0.581) |
0.0717 (1.00) |
Del Peak 24(10q21 1) | 82 (20%) | 331 |
0.959 (1.00) |
0.0528 (1.00) |
0.388 (1.00) |
0.0995 (1.00) |
0.955 (1.00) |
0.00841 (1.00) |
0.0976 (1.00) |
0.0193 (1.00) |
0.102 (1.00) |
Del Peak 25(10q23 31) | 94 (23%) | 319 |
0.834 (1.00) |
0.0124 (1.00) |
0.483 (1.00) |
0.164 (1.00) |
0.505 (1.00) |
0.00542 (1.00) |
0.00814 (1.00) |
0.0217 (1.00) |
0.131 (1.00) |
Del Peak 26(10q25 2) | 93 (23%) | 320 |
0.313 (1.00) |
0.164 (1.00) |
0.907 (1.00) |
0.164 (1.00) |
0.222 (1.00) |
0.00362 (1.00) |
0.0681 (1.00) |
0.0166 (1.00) |
0.129 (1.00) |
Del Peak 27(12p13 2) | 44 (11%) | 369 |
0.384 (1.00) |
0.633 (1.00) |
0.338 (1.00) |
0.00188 (1.00) |
0.899 (1.00) |
0.0827 (1.00) |
0.166 (1.00) |
0.0936 (1.00) |
1 (1.00) |
Del Peak 29(14q32 11) | 133 (32%) | 280 |
0.353 (1.00) |
0.506 (1.00) |
0.674 (1.00) |
0.000917 (0.518) |
0.634 (1.00) |
0.0616 (1.00) |
0.0367 (1.00) |
0.00428 (1.00) |
0.554 (1.00) |
Del Peak 30(15q11 2) | 160 (39%) | 253 |
0.93 (1.00) |
0.852 (1.00) |
1 (1.00) |
0.0238 (1.00) |
0.916 (1.00) |
0.0112 (1.00) |
0.0635 (1.00) |
0.00316 (1.00) |
0.0575 (1.00) |
Del Peak 31(15q21 1) | 151 (37%) | 262 |
0.0937 (1.00) |
0.658 (1.00) |
0.919 (1.00) |
0.0488 (1.00) |
0.97 (1.00) |
0.0832 (1.00) |
0.0887 (1.00) |
0.0555 (1.00) |
0.0483 (1.00) |
Del Peak 32(15q22 33) | 145 (35%) | 268 |
0.255 (1.00) |
0.426 (1.00) |
0.918 (1.00) |
0.00592 (1.00) |
0.583 (1.00) |
0.0426 (1.00) |
0.0478 (1.00) |
0.0216 (1.00) |
0.0427 (1.00) |
Del Peak 33(16p13 3) | 45 (11%) | 368 |
0.00179 (0.993) |
0.426 (1.00) |
0.755 (1.00) |
1 (1.00) |
0.0342 (1.00) |
0.0628 (1.00) |
0.357 (1.00) |
0.162 (1.00) |
1 (1.00) |
Del Peak 34(16q23 1) | 49 (12%) | 364 |
0.00129 (0.722) |
0.288 (1.00) |
0.129 (1.00) |
0.261 (1.00) |
0.63 (1.00) |
0.389 (1.00) |
0.979 (1.00) |
0.905 (1.00) |
1 (1.00) |
Del Peak 36(17q24 3) | 59 (14%) | 354 |
0.729 (1.00) |
0.51 (1.00) |
0.328 (1.00) |
1 (1.00) |
0.682 (1.00) |
0.00818 (1.00) |
0.253 (1.00) |
0.0319 (1.00) |
1 (1.00) |
Del Peak 42(20p12 1) | 79 (19%) | 334 |
0.803 (1.00) |
0.439 (1.00) |
0.618 (1.00) |
0.137 (1.00) |
0.697 (1.00) |
0.569 (1.00) |
0.983 (1.00) |
0.417 (1.00) |
1 (1.00) |
Del Peak 43(21q11 2) | 125 (30%) | 288 |
0.468 (1.00) |
0.722 (1.00) |
1 (1.00) |
0.0101 (1.00) |
0.269 (1.00) |
0.0408 (1.00) |
0.344 (1.00) |
0.187 (1.00) |
0.219 (1.00) |
Del Peak 44(22q13 32) | 138 (33%) | 275 |
0.208 (1.00) |
0.701 (1.00) |
0.603 (1.00) |
0.00499 (1.00) |
0.734 (1.00) |
0.00263 (1.00) |
0.0348 (1.00) |
0.0137 (1.00) |
1 (1.00) |
P value = 8.87e-07 (Fisher's exact test), Q value = 0.00054
Table S1. Gene #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 Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

P value = 8.13e-06 (Fisher's exact test), Q value = 0.0049
Table S2. Gene #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 Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

P value = 0.000308 (Fisher's exact test), Q value = 0.18
Table S3. Gene #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 Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

P value = 0.000133 (Fisher's exact test), Q value = 0.078
Table S4. Gene #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 Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

P value = 0.000155 (Fisher's exact test), Q value = 0.091
Table S5. Gene #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 Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

P value = 0.000188 (Fisher's exact test), Q value = 0.11
Table S6. Gene #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 Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.017
Table S7. Gene #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 Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

P value = 7.66e-06 (Fisher's exact test), Q value = 0.0046
Table S8. Gene #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 Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.00083
Table S9. Gene #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 Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

P value = 4.8e-06 (Fisher's exact test), Q value = 0.0029
Table S10. Gene #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 Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

P value = 0.000122 (Chi-square test), Q value = 0.072
Table S11. Gene #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 Gene #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

P value = 0.000411 (logrank test), Q value = 0.24
Table S12. Gene #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 Gene #30: 'Del Peak 6(3p26.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

P value = 0.00024 (logrank test), Q value = 0.14
Table S13. Gene #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 Gene #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

P value = 0.000257 (Fisher's exact test), Q value = 0.15
Table S14. Gene #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 Gene #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

P value = 0.000266 (Chi-square test), Q value = 0.16
Table S15. Gene #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 Gene #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

P value = 5.21e-05 (Fisher's exact test), Q value = 0.031
Table S16. Gene #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 Gene #37: 'Del Peak 13(5q21.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

P value = 0.000318 (Fisher's exact test), Q value = 0.18
Table S17. Gene #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 Gene #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

P value = 9.03e-05 (Fisher's exact test), Q value = 0.053
Table S18. Gene #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 Gene #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

P value = 8.04e-06 (Fisher's exact test), Q value = 0.0048
Table S19. Gene #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 Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

P value = 2.07e-07 (Fisher's exact test), Q value = 0.00013
Table S20. Gene #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 Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

P value = 0.000288 (Fisher's exact test), Q value = 0.17
Table S21. Gene #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 Gene #45: 'Del Peak 21(8p11.21) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

P value = 4.33e-05 (Chi-square test), Q value = 0.026
Table S22. Gene #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 Gene #52: 'Del Peak 28(13q14.13) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

P value = 3.38e-06 (Fisher's exact test), Q value = 0.002
Table S23. Gene #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 Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

P value = 2.62e-05 (Fisher's exact test), Q value = 0.016
Table S24. Gene #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 Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00069
Table S25. Gene #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 Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

P value = 8.39e-11 (Fisher's exact test), Q value = 5.1e-08
Table S26. Gene #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 Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

P value = 3.02e-10 (Fisher's exact test), Q value = 1.8e-07
Table S27. Gene #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 Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

P value = 0.000369 (Fisher's exact test), Q value = 0.21
Table S28. Gene #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 Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

P value = 3.87e-09 (Fisher's exact test), Q value = 2.4e-06
Table S29. Gene #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 Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

P value = 0.000105 (Fisher's exact test), Q value = 0.062
Table S30. Gene #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 Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

P value = 8.87e-06 (Fisher's exact test), Q value = 0.0053
Table S31. Gene #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 Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

P value = 4.48e-10 (Fisher's exact test), Q value = 2.7e-07
Table S32. Gene #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 Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

P value = 0.000105 (Fisher's exact test), Q value = 0.062
Table S33. Gene #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 Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.012
Table S34. Gene #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 Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

P value = 5.5e-05 (Fisher's exact test), Q value = 0.033
Table S35. Gene #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 Gene #65: 'Del Peak 41(19p13.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

-
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 = COAD-TP.clin.merged.picked.txt
-
Number of patients = 413
-
Number of copy number variation regions = 68
-
Number of selected clinical features = 9
-
Exclude regions that fewer than K tumors have alterations, K = 3
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
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
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
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
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.