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 10 clinical features across 413 patients, 34 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 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'.
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NEOADJUVANT THERAPY |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
Del Peak 9(4p16 2) | 121 (29%) | 292 |
0.00024 (0.157) |
0.609 (1.00) |
0.59 (1.00) |
0.036 (1.00) |
0.671 (1.00) |
0.000257 (0.168) |
0.000266 (0.173) |
0.000571 (0.365) |
0.0247 (1.00) |
0.877 (1.00) |
Del Peak 35(17p12) | 229 (55%) | 184 |
0.334 (1.00) |
0.0108 (1.00) |
0.43 (1.00) |
3.38e-06 (0.00227) |
0.868 (1.00) |
2.62e-05 (0.0174) |
0.0165 (1.00) |
1.15e-06 (0.000772) |
0.257 (1.00) |
0.2 (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 (2.62e-06) |
0.813 (1.00) |
0.000105 (0.0694) |
0.00624 (1.00) |
8.87e-06 (0.00592) |
0.299 (1.00) |
0.558 (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 (3.04e-07) |
0.813 (1.00) |
0.000105 (0.0694) |
0.00624 (1.00) |
1.94e-05 (0.0129) |
0.299 (1.00) |
0.77 (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 (0.00543) |
1 (1.00) |
0.00146 (0.912) |
0.00698 (1.00) |
0.000308 (0.2) |
0.288 (1.00) |
0.562 (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 (0.0872) |
0.323 (1.00) |
0.000155 (0.102) |
1 (1.00) |
0.156 (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 (0.123) |
0.18 (1.00) |
2.82e-05 (0.0188) |
0.574 (1.00) |
0.0713 (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 (0.206) |
0.0225 (1.00) |
9.03e-05 (0.0596) |
0.572 (1.00) |
0.154 (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 (0.00538) |
0.00136 (0.855) |
2.07e-07 (0.00014) |
0.589 (1.00) |
0.0898 (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 (2.05e-07) |
0.84 (1.00) |
0.00201 (1.00) |
0.0125 (1.00) |
0.000369 (0.239) |
0.277 (1.00) |
0.773 (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 (0.000598) |
0.972 (1.00) |
0.00316 (1.00) |
0.00471 (1.00) |
0.000458 (0.295) |
0.282 (1.00) |
0.47 (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 (0.00513) |
0.541 (1.00) |
0.0241 (1.00) |
0.0102 (1.00) |
0.000849 (0.54) |
0.562 (1.00) |
1 (1.00) |
Amp Peak 23(20q12) | 297 (72%) | 116 |
0.365 (1.00) |
0.51 (1.00) |
0.324 (1.00) |
1.38e-06 (0.000926) |
0.676 (1.00) |
0.0286 (1.00) |
0.00474 (1.00) |
0.00057 (0.365) |
0.563 (1.00) |
0.754 (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 (0.00322) |
0.641 (1.00) |
0.0179 (1.00) |
0.00667 (1.00) |
0.000552 (0.354) |
0.565 (1.00) |
0.874 (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 (0.08) |
0.000869 (0.551) |
1 (1.00) |
0.243 (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 (0.0345) |
0.0201 (1.00) |
0.000559 (0.358) |
0.0223 (1.00) |
0.0855 (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 (0.187) |
0.00793 (1.00) |
0.000868 (0.551) |
0.282 (1.00) |
0.644 (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 (0.0287) |
0.851 (1.00) |
1 (1.00) |
0.489 (1.00) |
Del Peak 37(18p11 31) | 220 (53%) | 193 |
0.869 (1.00) |
0.0199 (1.00) |
1 (1.00) |
8.39e-11 (5.71e-08) |
0.822 (1.00) |
0.0483 (1.00) |
0.00385 (1.00) |
0.00179 (1.00) |
0.251 (1.00) |
0.778 (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 (0.0363) |
0.0321 (1.00) |
0.00155 (0.968) |
0.36 (1.00) |
0.838 (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) |
0.206 (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) |
0.723 (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) |
0.812 (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 (0.882) |
0.609 (1.00) |
0.0104 (1.00) |
0.00974 (1.00) |
0.392 (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) |
0.656 (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) |
0.668 (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) |
0.202 (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) |
0.39 (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) |
1 (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) |
0.145 (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) |
0.00513 (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) |
0.000501 (0.322) |
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) |
0.00146 (0.912) |
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) |
0.0758 (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) |
0.395 (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) |
0.259 (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) |
0.478 (1.00) |
Del Peak 2(1p33) | 107 (26%) | 306 |
0.00122 (0.766) |
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) |
0.419 (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 (0.634) |
0.000797 (0.508) |
0.00853 (1.00) |
1 (1.00) |
0.513 (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) |
0.818 (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) |
0.056 (1.00) |
Del Peak 6(3p26 1) | 60 (15%) | 353 |
0.000411 (0.266) |
0.346 (1.00) |
1 (1.00) |
0.146 (1.00) |
0.0576 (1.00) |
0.0189 (1.00) |
0.000457 (0.295) |
0.000506 (0.325) |
1 (1.00) |
0.547 (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) |
0.584 (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) |
0.63 (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 (1.00) |
0.118 (1.00) |
0.0167 (1.00) |
0.0279 (1.00) |
0.539 (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) |
0.176 (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) |
0.0873 (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) |
0.521 (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) |
0.4 (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) |
0.69 (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) |
0.191 (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 (0.556) |
0.0887 (1.00) |
0.00256 (1.00) |
0.0973 (1.00) |
0.209 (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) |
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 (1.00) |
0.00231 (1.00) |
0.00103 (0.65) |
0.0717 (1.00) |
0.343 (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) |
0.378 (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) |
0.0625 (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) |
0.501 (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) |
0.818 (1.00) |
Del Peak 29(14q32 11) | 133 (32%) | 280 |
0.353 (1.00) |
0.506 (1.00) |
0.674 (1.00) |
0.000917 (0.579) |
0.634 (1.00) |
0.0616 (1.00) |
0.0367 (1.00) |
0.00428 (1.00) |
0.554 (1.00) |
0.652 (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) |
0.471 (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) |
0.463 (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) |
0.657 (1.00) |
Del Peak 33(16p13 3) | 45 (11%) | 368 |
0.00179 (1.00) |
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) |
0.82 (1.00) |
Del Peak 34(16q23 1) | 49 (12%) | 364 |
0.00129 (0.808) |
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) |
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) |
0.227 (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) |
0.721 (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) |
0.538 (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) |
0.765 (1.00) |
P value = 8.87e-07 (Fisher's exact test), Q value = 6e-04
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 |
P value = 8.13e-06 (Fisher's exact test), Q value = 0.0054
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 |
P value = 0.000308 (Fisher's exact test), Q value = 0.2
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 |
P value = 0.000133 (Fisher's exact test), Q value = 0.087
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 |
P value = 0.000155 (Fisher's exact test), Q value = 0.1
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 |
P value = 0.000188 (Fisher's exact test), Q value = 0.12
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 |
P value = 2.82e-05 (Fisher's exact test), Q value = 0.019
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 |
P value = 7.66e-06 (Fisher's exact test), Q value = 0.0051
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 |
P value = 1.38e-06 (Fisher's exact test), Q value = 0.00093
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
AMP PEAK 23(20Q12) MUTATED | 271 | 23 |
AMP PEAK 23(20Q12) WILD-TYPE | 85 | 31 |
P value = 4.8e-06 (Fisher's exact test), Q value = 0.0032
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 |
P value = 0.000122 (Chi-square test), Q value = 0.08
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 |
P value = 0.00024 (logrank test), Q value = 0.16
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) |
P value = 0.000257 (Fisher's exact test), Q value = 0.17
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 |
P value = 0.000266 (Chi-square test), Q value = 0.17
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 |
P value = 5.21e-05 (Fisher's exact test), Q value = 0.034
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 |
P value = 0.000318 (Fisher's exact test), Q value = 0.21
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 |
P value = 9.03e-05 (Fisher's exact test), Q value = 0.06
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 |
P value = 8.04e-06 (Fisher's exact test), Q value = 0.0054
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 |
P value = 2.07e-07 (Fisher's exact test), Q value = 0.00014
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 |
P value = 0.000288 (Fisher's exact test), Q value = 0.19
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 |
P value = 4.33e-05 (Chi-square test), Q value = 0.029
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 |
P value = 3.38e-06 (Fisher's exact test), Q value = 0.0023
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
DEL PEAK 35(17P12) MUTATED | 213 | 14 |
DEL PEAK 35(17P12) WILD-TYPE | 143 | 40 |
P value = 2.62e-05 (Fisher's exact test), Q value = 0.017
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 |
P value = 1.15e-06 (Fisher's exact test), Q value = 0.00077
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 |
P value = 8.39e-11 (Fisher's exact test), Q value = 5.7e-08
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 |
P value = 3.02e-10 (Fisher's exact test), Q value = 2e-07
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 |
P value = 0.000369 (Fisher's exact test), Q value = 0.24
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 |
P value = 3.87e-09 (Fisher's exact test), Q value = 2.6e-06
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 |
P value = 0.000105 (Fisher's exact test), Q value = 0.069
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 |
P value = 8.87e-06 (Fisher's exact test), Q value = 0.0059
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 |
P value = 4.48e-10 (Fisher's exact test), Q value = 3e-07
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 |
P value = 0.000105 (Fisher's exact test), Q value = 0.069
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 |
P value = 1.94e-05 (Fisher's exact test), Q value = 0.013
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 |
P value = 5.5e-05 (Fisher's exact test), Q value = 0.036
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 |
-
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.clin.merged.picked.txt
-
Number of patients = 413
-
Number of copy number variation regions = 68
-
Number of selected clinical features = 10
-
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.