This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 75 arm-level results and 12 clinical features across 575 patients, 35 significant findings detected with Q value < 0.25.
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Amp Peak 2(2q33.1) cnv correlated to 'LYMPH.NODE.METASTASIS'.
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Amp Peak 6(7p21.3) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Amp Peak 11(10q22.3) cnv correlated to 'LYMPH.NODE.METASTASIS'.
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Amp Peak 14(13q12.13) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Amp Peak 15(13q12.2) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Amp Peak 16(13q22.1) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Amp Peak 24(20p11.21) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Amp Peak 25(20q11.21) cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
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Amp Peak 26(20q12) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'NEOPLASM.DISEASESTAGE'.
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Amp Peak 27(20q13.32) cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
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Del Peak 10(4p16.1) cnv correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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Del Peak 18(8p23.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'LYMPH.NODE.METASTASIS'.
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Del Peak 19(8p22) cnv correlated to 'HISTOLOGICAL.TYPE', 'LYMPH.NODE.METASTASIS', and 'NUMBER.OF.LYMPH.NODES'.
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Del Peak 30(14q22.1) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Del Peak 34(16p13.3) cnv correlated to 'Time to Death'.
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Del Peak 36(17p12) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Del Peak 38(18p11.31) cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
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Del Peak 39(18q12.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
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Del Peak 40(18q21.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'LYMPH.NODE.METASTASIS', and 'NEOPLASM.DISEASESTAGE'.
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Del Peak 41(18q22.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'NEOPLASM.DISEASESTAGE'.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
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 | Chi-square test | Fisher's exact test | t-test | t-test | Chi-square test | |
Del Peak 40(18q21 2) | 0 (0%) | 172 |
0.493 (1.00) |
0.0823 (1.00) |
1.07e-09 (8.75e-07) |
0.144 (1.00) |
3.54e-16 (2.92e-13) |
0.0637 (1.00) |
0.0015 (1.00) |
0.000227 (0.18) |
0.0558 (1.00) |
0.00113 (0.864) |
4.49e-05 (0.0359) |
|
Amp Peak 26(20q12) | 0 (0%) | 134 |
0.268 (1.00) |
0.726 (1.00) |
4.74e-06 (0.00383) |
0.325 (1.00) |
5.41e-13 (4.44e-10) |
0.692 (1.00) |
0.00133 (1.00) |
0.0446 (1.00) |
0.0683 (1.00) |
0.385 (1.00) |
0.00019 (0.151) |
|
Del Peak 18(8p23 2) | 0 (0%) | 303 |
0.606 (1.00) |
0.205 (1.00) |
2.4e-05 (0.0193) |
0.155 (1.00) |
2.72e-05 (0.0219) |
0.0155 (1.00) |
0.00935 (1.00) |
0.000164 (0.13) |
0.00768 (1.00) |
0.000456 (0.358) |
0.00132 (1.00) |
|
Del Peak 19(8p22) | 0 (0%) | 290 |
0.581 (1.00) |
0.317 (1.00) |
0.000379 (0.299) |
0.358 (1.00) |
0.000245 (0.194) |
0.0196 (1.00) |
0.00357 (1.00) |
1.79e-05 (0.0144) |
0.0104 (1.00) |
0.000114 (0.0912) |
0.00037 (0.292) |
|
Del Peak 41(18q22 1) | 0 (0%) | 177 |
0.343 (1.00) |
0.221 (1.00) |
1.94e-07 (0.000158) |
0.206 (1.00) |
2.05e-15 (1.68e-12) |
0.0632 (1.00) |
0.00221 (1.00) |
0.00177 (1.00) |
0.108 (1.00) |
0.00209 (1.00) |
0.000104 (0.0831) |
|
Amp Peak 25(20q11 21) | 0 (0%) | 136 |
0.31 (1.00) |
0.823 (1.00) |
9.13e-06 (0.00737) |
0.327 (1.00) |
7.95e-12 (6.52e-09) |
0.693 (1.00) |
0.00547 (1.00) |
0.0526 (1.00) |
0.0685 (1.00) |
0.337 (1.00) |
0.000699 (0.541) |
|
Amp Peak 27(20q13 32) | 0 (0%) | 131 |
0.361 (1.00) |
0.658 (1.00) |
2.18e-05 (0.0175) |
0.55 (1.00) |
8.79e-12 (7.2e-09) |
0.692 (1.00) |
0.00436 (1.00) |
0.0501 (1.00) |
0.0671 (1.00) |
0.24 (1.00) |
0.000657 (0.509) |
|
Del Peak 38(18p11 31) | 0 (0%) | 234 |
0.976 (1.00) |
0.059 (1.00) |
1.82e-06 (0.00148) |
0.932 (1.00) |
1.52e-16 (1.25e-13) |
0.322 (1.00) |
0.000547 (0.429) |
0.138 (1.00) |
0.0199 (1.00) |
0.487 (1.00) |
0.00232 (1.00) |
|
Del Peak 39(18q12 2) | 0 (0%) | 189 |
0.923 (1.00) |
0.0817 (1.00) |
1.57e-09 (1.28e-06) |
0.424 (1.00) |
8.26e-18 (6.82e-15) |
0.034 (1.00) |
0.00422 (1.00) |
0.00484 (1.00) |
0.056 (1.00) |
0.00963 (1.00) |
0.000584 (0.456) |
|
Amp Peak 2(2q33 1) | 0 (0%) | 452 |
0.129 (1.00) |
0.385 (1.00) |
0.031 (1.00) |
1 (1.00) |
0.00372 (1.00) |
0.103 (1.00) |
0.535 (1.00) |
0.000238 (0.188) |
0.397 (1.00) |
0.0257 (1.00) |
0.0255 (1.00) |
|
Amp Peak 6(7p21 3) | 0 (0%) | 238 |
0.294 (1.00) |
0.103 (1.00) |
0.0292 (1.00) |
0.671 (1.00) |
0.000225 (0.179) |
0.0882 (1.00) |
0.0259 (1.00) |
0.000569 (0.445) |
0.148 (1.00) |
0.0314 (1.00) |
0.000392 (0.308) |
|
Amp Peak 11(10q22 3) | 0 (0%) | 540 |
0.819 (1.00) |
0.303 (1.00) |
1 (1.00) |
0.488 (1.00) |
0.931 (1.00) |
0.434 (1.00) |
0.911 (1.00) |
2.77e-05 (0.0222) |
0.919 (1.00) |
0.087 (1.00) |
0.464 (1.00) |
|
Amp Peak 14(13q12 13) | 0 (0%) | 204 |
0.122 (1.00) |
0.314 (1.00) |
0.00246 (1.00) |
0.663 (1.00) |
1.21e-09 (9.85e-07) |
1 (1.00) |
0.0104 (1.00) |
0.00114 (0.868) |
0.0545 (1.00) |
0.031 (1.00) |
0.000587 (0.458) |
|
Amp Peak 15(13q12 2) | 0 (0%) | 209 |
0.0977 (1.00) |
0.239 (1.00) |
0.00188 (1.00) |
0.487 (1.00) |
2.65e-09 (2.16e-06) |
1 (1.00) |
0.0238 (1.00) |
0.00237 (1.00) |
0.0962 (1.00) |
0.0323 (1.00) |
0.00161 (1.00) |
|
Amp Peak 16(13q22 1) | 0 (0%) | 204 |
0.0436 (1.00) |
0.444 (1.00) |
0.0249 (1.00) |
0.191 (1.00) |
3.25e-08 (2.65e-05) |
0.503 (1.00) |
0.0248 (1.00) |
0.000608 (0.474) |
0.284 (1.00) |
0.172 (1.00) |
0.0118 (1.00) |
|
Amp Peak 24(20p11 21) | 0 (0%) | 236 |
0.806 (1.00) |
0.709 (1.00) |
0.00784 (1.00) |
0.0505 (1.00) |
1.14e-05 (0.00919) |
0.32 (1.00) |
0.00329 (1.00) |
0.691 (1.00) |
0.68 (1.00) |
0.923 (1.00) |
0.0374 (1.00) |
|
Del Peak 10(4p16 1) | 0 (0%) | 393 |
0.0429 (1.00) |
0.954 (1.00) |
0.0561 (1.00) |
0.106 (1.00) |
0.0275 (1.00) |
2.78e-05 (0.0222) |
0.0125 (1.00) |
0.00495 (1.00) |
0.0508 (1.00) |
0.00162 (1.00) |
0.00639 (1.00) |
|
Del Peak 30(14q22 1) | 0 (0%) | 390 |
0.211 (1.00) |
0.233 (1.00) |
0.0212 (1.00) |
0.422 (1.00) |
1.15e-06 (0.00093) |
0.725 (1.00) |
0.143 (1.00) |
0.0171 (1.00) |
0.856 (1.00) |
0.693 (1.00) |
0.552 (1.00) |
|
Del Peak 34(16p13 3) | 0 (0%) | 517 |
8.33e-05 (0.0666) |
0.254 (1.00) |
0.359 (1.00) |
0.89 (1.00) |
0.421 (1.00) |
0.609 (1.00) |
0.38 (1.00) |
0.179 (1.00) |
0.797 (1.00) |
0.059 (1.00) |
0.0498 (1.00) |
|
Del Peak 36(17p12) | 0 (0%) | 232 |
0.674 (1.00) |
0.0983 (1.00) |
0.00169 (1.00) |
0.551 (1.00) |
6.55e-08 (5.33e-05) |
0.325 (1.00) |
0.0397 (1.00) |
0.000609 (0.474) |
0.261 (1.00) |
0.00263 (1.00) |
0.00229 (1.00) |
|
Amp Peak 1(1q31 1) | 0 (0%) | 441 |
0.454 (1.00) |
0.292 (1.00) |
0.0268 (1.00) |
0.198 (1.00) |
0.0927 (1.00) |
0.0357 (1.00) |
0.171 (1.00) |
0.0195 (1.00) |
0.632 (1.00) |
0.0141 (1.00) |
0.327 (1.00) |
|
Amp Peak 3(5p12) | 0 (0%) | 468 |
0.015 (1.00) |
0.372 (1.00) |
0.151 (1.00) |
0.83 (1.00) |
0.056 (1.00) |
0.379 (1.00) |
0.349 (1.00) |
0.113 (1.00) |
0.037 (1.00) |
0.0665 (1.00) |
0.164 (1.00) |
|
Amp Peak 4(5q22 3) | 0 (0%) | 516 |
0.757 (1.00) |
0.865 (1.00) |
0.445 (1.00) |
0.891 (1.00) |
0.315 (1.00) |
1 (1.00) |
0.0314 (1.00) |
0.23 (1.00) |
0.0768 (1.00) |
0.476 (1.00) |
0.505 (1.00) |
|
Amp Peak 5(6p21 1) | 0 (0%) | 429 |
0.476 (1.00) |
0.682 (1.00) |
0.0314 (1.00) |
0.151 (1.00) |
0.00234 (1.00) |
0.00136 (1.00) |
0.106 (1.00) |
0.000788 (0.608) |
0.176 (1.00) |
0.0025 (1.00) |
0.0197 (1.00) |
|
Amp Peak 7(8p11 23) | 0 (0%) | 379 |
0.458 (1.00) |
0.752 (1.00) |
0.625 (1.00) |
0.428 (1.00) |
0.238 (1.00) |
0.498 (1.00) |
0.426 (1.00) |
0.456 (1.00) |
0.169 (1.00) |
0.634 (1.00) |
0.172 (1.00) |
|
Amp Peak 8(8p11 21) | 0 (0%) | 337 |
0.653 (1.00) |
0.597 (1.00) |
0.636 (1.00) |
0.175 (1.00) |
0.122 (1.00) |
0.742 (1.00) |
0.316 (1.00) |
0.301 (1.00) |
0.047 (1.00) |
0.429 (1.00) |
0.126 (1.00) |
|
Amp Peak 9(8q12 1) | 0 (0%) | 266 |
0.92 (1.00) |
0.19 (1.00) |
0.303 (1.00) |
0.557 (1.00) |
0.0095 (1.00) |
0.0423 (1.00) |
0.027 (1.00) |
0.171 (1.00) |
0.107 (1.00) |
0.0282 (1.00) |
0.0546 (1.00) |
|
Amp Peak 10(8q24 21) | 0 (0%) | 230 |
0.531 (1.00) |
0.236 (1.00) |
0.0863 (1.00) |
0.349 (1.00) |
0.0112 (1.00) |
0.0931 (1.00) |
0.0571 (1.00) |
0.569 (1.00) |
0.215 (1.00) |
0.0656 (1.00) |
0.144 (1.00) |
|
Amp Peak 12(11p15 5) | 0 (0%) | 446 |
0.711 (1.00) |
0.0608 (1.00) |
0.145 (1.00) |
0.548 (1.00) |
0.00145 (1.00) |
0.12 (1.00) |
0.383 (1.00) |
0.809 (1.00) |
0.878 (1.00) |
0.429 (1.00) |
0.99 (1.00) |
|
Amp Peak 13(12p13 32) | 0 (0%) | 431 |
0.257 (1.00) |
0.0696 (1.00) |
0.829 (1.00) |
0.501 (1.00) |
0.336 (1.00) |
0.698 (1.00) |
0.0847 (1.00) |
0.446 (1.00) |
0.744 (1.00) |
0.447 (1.00) |
0.158 (1.00) |
|
Amp Peak 17(15q26 1) | 0 (0%) | 532 |
0.0799 (1.00) |
0.753 (1.00) |
0.291 (1.00) |
0.0573 (1.00) |
0.429 (1.00) |
0.141 (1.00) |
0.649 (1.00) |
0.0323 (1.00) |
0.602 (1.00) |
0.0547 (1.00) |
0.124 (1.00) |
|
Amp Peak 18(16p11 2) | 0 (0%) | 414 |
0.843 (1.00) |
0.26 (1.00) |
0.918 (1.00) |
0.643 (1.00) |
0.00247 (1.00) |
0.715 (1.00) |
0.108 (1.00) |
0.00225 (1.00) |
0.278 (1.00) |
0.0162 (1.00) |
0.000886 (0.682) |
|
Amp Peak 19(17q12) | 0 (0%) | 431 |
0.492 (1.00) |
0.363 (1.00) |
0.591 (1.00) |
0.102 (1.00) |
0.456 (1.00) |
0.462 (1.00) |
0.0112 (1.00) |
0.0123 (1.00) |
0.0732 (1.00) |
0.351 (1.00) |
0.155 (1.00) |
|
Amp Peak 20(17q24 1) | 0 (0%) | 447 |
0.0404 (1.00) |
0.245 (1.00) |
0.911 (1.00) |
0.616 (1.00) |
0.0884 (1.00) |
0.691 (1.00) |
0.0535 (1.00) |
0.0443 (1.00) |
0.232 (1.00) |
0.711 (1.00) |
0.483 (1.00) |
|
Amp Peak 21(19p13 2) | 0 (0%) | 478 |
0.14 (1.00) |
0.493 (1.00) |
0.216 (1.00) |
0.219 (1.00) |
0.0514 (1.00) |
1 (1.00) |
0.23 (1.00) |
0.219 (1.00) |
0.119 (1.00) |
0.994 (1.00) |
0.578 (1.00) |
|
Amp Peak 22(19q12) | 0 (0%) | 453 |
0.625 (1.00) |
0.941 (1.00) |
0.256 (1.00) |
0.22 (1.00) |
0.0292 (1.00) |
0.692 (1.00) |
0.135 (1.00) |
0.583 (1.00) |
0.474 (1.00) |
0.403 (1.00) |
0.785 (1.00) |
|
Amp Peak 23(20p11 23) | 0 (0%) | 274 |
0.702 (1.00) |
0.921 (1.00) |
0.0194 (1.00) |
0.0446 (1.00) |
0.00073 (0.563) |
0.181 (1.00) |
0.00143 (1.00) |
0.169 (1.00) |
0.382 (1.00) |
0.295 (1.00) |
0.00642 (1.00) |
|
Amp Peak 28(Xq28) | 0 (0%) | 454 |
0.252 (1.00) |
0.209 (1.00) |
0.421 (1.00) |
0.758 (1.00) |
0.0252 (1.00) |
0.693 (1.00) |
0.228 (1.00) |
0.0168 (1.00) |
0.358 (1.00) |
0.271 (1.00) |
0.0707 (1.00) |
|
Del Peak 1(1p36 11) | 0 (0%) | 353 |
0.0525 (1.00) |
0.105 (1.00) |
0.126 (1.00) |
0.345 (1.00) |
0.0065 (1.00) |
0.739 (1.00) |
0.000579 (0.453) |
0.0134 (1.00) |
0.102 (1.00) |
0.000524 (0.411) |
0.0263 (1.00) |
|
Del Peak 2(1p33) | 0 (0%) | 419 |
0.0185 (1.00) |
0.836 (1.00) |
0.401 (1.00) |
0.851 (1.00) |
0.079 (1.00) |
0.709 (1.00) |
0.0103 (1.00) |
0.0233 (1.00) |
0.314 (1.00) |
0.0143 (1.00) |
0.022 (1.00) |
|
Del Peak 3(1p13 2) | 0 (0%) | 418 |
0.072 (1.00) |
0.841 (1.00) |
0.248 (1.00) |
0.64 (1.00) |
0.135 (1.00) |
0.265 (1.00) |
0.00123 (0.933) |
0.00247 (1.00) |
0.243 (1.00) |
0.00268 (1.00) |
0.00657 (1.00) |
|
Del Peak 4(2p12) | 0 (0%) | 555 |
0.81 (1.00) |
0.179 (1.00) |
0.00346 (1.00) |
0.821 (1.00) |
0.0206 (1.00) |
0.275 (1.00) |
0.56 (1.00) |
0.882 (1.00) |
0.885 (1.00) |
0.315 (1.00) |
0.358 (1.00) |
|
Del Peak 5(2q22 1) | 0 (0%) | 542 |
0.855 (1.00) |
0.564 (1.00) |
0.842 (1.00) |
0.474 (1.00) |
0.927 (1.00) |
1 (1.00) |
0.691 (1.00) |
0.829 (1.00) |
1 (1.00) |
0.912 (1.00) |
0.474 (1.00) |
|
Del Peak 6(2q37 2) | 0 (0%) | 545 |
0.845 (1.00) |
0.139 (1.00) |
0.835 (1.00) |
0.456 (1.00) |
0.944 (1.00) |
1 (1.00) |
0.134 (1.00) |
0.73 (1.00) |
0.398 (1.00) |
0.867 (1.00) |
0.273 (1.00) |
|
Del Peak 7(3p26 3) | 0 (0%) | 491 |
0.000649 (0.504) |
0.855 (1.00) |
0.691 (1.00) |
0.723 (1.00) |
0.193 (1.00) |
0.131 (1.00) |
0.00101 (0.778) |
0.0172 (1.00) |
0.0636 (1.00) |
0.0284 (1.00) |
0.00837 (1.00) |
|
Del Peak 8(3p14 2) | 0 (0%) | 471 |
0.231 (1.00) |
0.578 (1.00) |
0.808 (1.00) |
0.665 (1.00) |
0.422 (1.00) |
0.669 (1.00) |
0.031 (1.00) |
0.213 (1.00) |
0.173 (1.00) |
0.0248 (1.00) |
0.144 (1.00) |
|
Del Peak 9(3q26 31) | 0 (0%) | 519 |
0.704 (1.00) |
0.996 (1.00) |
0.874 (1.00) |
0.12 (1.00) |
0.0425 (1.00) |
0.216 (1.00) |
0.325 (1.00) |
0.0202 (1.00) |
0.191 (1.00) |
0.492 (1.00) |
0.00239 (1.00) |
|
Del Peak 11(4q22 1) | 0 (0%) | 377 |
0.197 (1.00) |
0.42 (1.00) |
0.00417 (1.00) |
0.188 (1.00) |
0.00139 (1.00) |
0.00114 (0.867) |
0.362 (1.00) |
0.00344 (1.00) |
0.713 (1.00) |
0.00265 (1.00) |
0.0535 (1.00) |
|
Del Peak 12(4q35 1) | 0 (0%) | 364 |
0.282 (1.00) |
0.303 (1.00) |
0.0325 (1.00) |
0.862 (1.00) |
0.0205 (1.00) |
0.00185 (1.00) |
0.638 (1.00) |
0.0674 (1.00) |
0.658 (1.00) |
0.024 (1.00) |
0.241 (1.00) |
|
Del Peak 13(5q11 2) | 0 (0%) | 435 |
0.159 (1.00) |
0.0866 (1.00) |
0.0389 (1.00) |
0.922 (1.00) |
0.0271 (1.00) |
0.00103 (0.789) |
0.0224 (1.00) |
0.0373 (1.00) |
0.595 (1.00) |
0.0234 (1.00) |
0.0266 (1.00) |
|
Del Peak 14(5q22 2) | 0 (0%) | 403 |
0.082 (1.00) |
0.359 (1.00) |
0.155 (1.00) |
0.524 (1.00) |
0.0622 (1.00) |
0.000382 (0.301) |
0.03 (1.00) |
0.0584 (1.00) |
0.21 (1.00) |
0.147 (1.00) |
0.0684 (1.00) |
|
Del Peak 15(6p25 3) | 0 (0%) | 497 |
0.599 (1.00) |
0.0683 (1.00) |
1 (1.00) |
0.0885 (1.00) |
0.546 (1.00) |
0.351 (1.00) |
0.324 (1.00) |
0.477 (1.00) |
0.329 (1.00) |
0.734 (1.00) |
0.664 (1.00) |
|
Del Peak 16(6q26) | 0 (0%) | 485 |
0.032 (1.00) |
0.9 (1.00) |
0.368 (1.00) |
0.302 (1.00) |
0.0479 (1.00) |
0.637 (1.00) |
0.038 (1.00) |
0.041 (1.00) |
0.0939 (1.00) |
0.0091 (1.00) |
0.109 (1.00) |
|
Del Peak 17(7q31 1) | 0 (0%) | 560 |
0.918 (1.00) |
0.329 (1.00) |
1 (1.00) |
0.305 (1.00) |
0.503 (1.00) |
1 (1.00) |
0.332 (1.00) |
0.696 (1.00) |
0.723 (1.00) |
0.606 (1.00) |
0.849 (1.00) |
|
Del Peak 20(8p11 21) | 0 (0%) | 451 |
0.599 (1.00) |
0.329 (1.00) |
0.031 (1.00) |
0.478 (1.00) |
0.163 (1.00) |
0.414 (1.00) |
0.0806 (1.00) |
0.0364 (1.00) |
0.117 (1.00) |
0.0914 (1.00) |
0.077 (1.00) |
|
Del Peak 21(8q11 1) | 0 (0%) | 531 |
0.891 (1.00) |
0.382 (1.00) |
0.16 (1.00) |
0.208 (1.00) |
0.413 (1.00) |
0.514 (1.00) |
0.00198 (1.00) |
0.047 (1.00) |
0.376 (1.00) |
0.292 (1.00) |
0.0335 (1.00) |
|
Del Peak 22(9p24 2) | 0 (0%) | 497 |
0.00182 (1.00) |
0.12 (1.00) |
0.496 (1.00) |
0.0513 (1.00) |
0.452 (1.00) |
0.351 (1.00) |
0.0227 (1.00) |
0.0662 (1.00) |
0.117 (1.00) |
0.228 (1.00) |
0.496 (1.00) |
|
Del Peak 23(10p15 3) | 0 (0%) | 473 |
0.548 (1.00) |
0.0282 (1.00) |
0.271 (1.00) |
0.913 (1.00) |
0.361 (1.00) |
0.00145 (1.00) |
0.178 (1.00) |
0.0241 (1.00) |
0.949 (1.00) |
0.0444 (1.00) |
0.0672 (1.00) |
|
Del Peak 24(10q21 1) | 0 (0%) | 457 |
0.852 (1.00) |
0.0152 (1.00) |
0.421 (1.00) |
0.535 (1.00) |
0.118 (1.00) |
0.00326 (1.00) |
0.681 (1.00) |
0.0945 (1.00) |
0.393 (1.00) |
0.163 (1.00) |
0.18 (1.00) |
|
Del Peak 25(10q23 31) | 0 (0%) | 430 |
0.553 (1.00) |
0.00668 (1.00) |
0.0408 (1.00) |
0.923 (1.00) |
0.0205 (1.00) |
0.0013 (0.986) |
0.0614 (1.00) |
0.0119 (1.00) |
0.491 (1.00) |
0.188 (1.00) |
0.0508 (1.00) |
|
Del Peak 26(10q25 2) | 0 (0%) | 435 |
0.779 (1.00) |
0.0715 (1.00) |
0.128 (1.00) |
0.846 (1.00) |
0.0322 (1.00) |
0.00103 (0.789) |
0.427 (1.00) |
0.0114 (1.00) |
0.459 (1.00) |
0.161 (1.00) |
0.165 (1.00) |
|
Del Peak 27(11q22 3) | 0 (0%) | 471 |
0.502 (1.00) |
0.396 (1.00) |
0.086 (1.00) |
0.587 (1.00) |
0.0522 (1.00) |
0.061 (1.00) |
0.654 (1.00) |
0.0114 (1.00) |
0.631 (1.00) |
0.0442 (1.00) |
0.759 (1.00) |
|
Del Peak 28(12p13 1) | 0 (0%) | 498 |
0.464 (1.00) |
0.472 (1.00) |
0.0256 (1.00) |
0.326 (1.00) |
0.000673 (0.521) |
0.344 (1.00) |
0.0985 (1.00) |
0.229 (1.00) |
0.768 (1.00) |
0.921 (1.00) |
0.589 (1.00) |
|
Del Peak 29(12q21 2) | 0 (0%) | 495 |
0.669 (1.00) |
0.709 (1.00) |
0.0779 (1.00) |
0.631 (1.00) |
0.00833 (1.00) |
0.117 (1.00) |
0.0906 (1.00) |
0.0551 (1.00) |
1 (1.00) |
0.0825 (1.00) |
0.0947 (1.00) |
|
Del Peak 31(15q11 2) | 0 (0%) | 342 |
0.77 (1.00) |
0.618 (1.00) |
0.216 (1.00) |
0.551 (1.00) |
0.0552 (1.00) |
0.035 (1.00) |
0.258 (1.00) |
0.0889 (1.00) |
0.888 (1.00) |
0.0606 (1.00) |
0.0877 (1.00) |
|
Del Peak 32(15q21 1) | 0 (0%) | 348 |
0.435 (1.00) |
0.603 (1.00) |
0.0355 (1.00) |
0.306 (1.00) |
0.0252 (1.00) |
0.0327 (1.00) |
0.222 (1.00) |
0.0842 (1.00) |
0.559 (1.00) |
0.0553 (1.00) |
0.218 (1.00) |
|
Del Peak 33(15q22 33) | 0 (0%) | 358 |
0.552 (1.00) |
0.327 (1.00) |
0.012 (1.00) |
0.73 (1.00) |
0.00583 (1.00) |
0.00229 (1.00) |
0.205 (1.00) |
0.058 (1.00) |
0.7 (1.00) |
0.0284 (1.00) |
0.013 (1.00) |
|
Del Peak 35(16q23 1) | 0 (0%) | 503 |
0.00152 (1.00) |
0.264 (1.00) |
0.402 (1.00) |
0.165 (1.00) |
0.508 (1.00) |
1 (1.00) |
0.95 (1.00) |
0.466 (1.00) |
0.941 (1.00) |
0.25 (1.00) |
0.322 (1.00) |
|
Del Peak 37(17q24 3) | 0 (0%) | 491 |
0.718 (1.00) |
0.305 (1.00) |
0.793 (1.00) |
0.124 (1.00) |
0.989 (1.00) |
0.626 (1.00) |
0.348 (1.00) |
0.00108 (0.827) |
0.316 (1.00) |
0.043 (1.00) |
0.123 (1.00) |
|
Del Peak 42(19p13 3) | 0 (0%) | 483 |
0.396 (1.00) |
0.183 (1.00) |
0.0305 (1.00) |
0.734 (1.00) |
0.0669 (1.00) |
0.641 (1.00) |
0.0269 (1.00) |
0.000979 (0.753) |
0.179 (1.00) |
0.00272 (1.00) |
0.002 (1.00) |
|
Del Peak 43(19q13 43) | 0 (0%) | 507 |
0.486 (1.00) |
0.816 (1.00) |
0.146 (1.00) |
0.247 (1.00) |
0.412 (1.00) |
0.289 (1.00) |
0.0703 (1.00) |
0.101 (1.00) |
0.812 (1.00) |
0.0188 (1.00) |
0.00724 (1.00) |
|
Del Peak 44(20p12 1) | 0 (0%) | 396 |
0.106 (1.00) |
0.631 (1.00) |
0.0445 (1.00) |
0.279 (1.00) |
0.14 (1.00) |
0.0632 (1.00) |
0.83 (1.00) |
0.623 (1.00) |
0.438 (1.00) |
0.793 (1.00) |
0.257 (1.00) |
|
Del Peak 45(20p12 1) | 0 (0%) | 396 |
0.106 (1.00) |
0.631 (1.00) |
0.0445 (1.00) |
0.279 (1.00) |
0.14 (1.00) |
0.0632 (1.00) |
0.83 (1.00) |
0.623 (1.00) |
0.438 (1.00) |
0.793 (1.00) |
0.257 (1.00) |
|
Del Peak 46(21q11 2) | 0 (0%) | 380 |
0.534 (1.00) |
0.721 (1.00) |
0.00555 (1.00) |
0.597 (1.00) |
0.000621 (0.482) |
0.175 (1.00) |
0.606 (1.00) |
0.307 (1.00) |
0.73 (1.00) |
0.00412 (1.00) |
0.379 (1.00) |
|
Del Peak 47(22q13 32) | 0 (0%) | 371 |
0.0441 (1.00) |
0.672 (1.00) |
0.173 (1.00) |
0.861 (1.00) |
0.0097 (1.00) |
0.727 (1.00) |
0.0266 (1.00) |
0.00237 (1.00) |
0.521 (1.00) |
0.0109 (1.00) |
0.036 (1.00) |
P value = 0.000238 (Chi-square test), Q value = 0.19
nPatients | N0 | N1 | N1A | N1B | N1C | N2 | N2A | N2B | NX |
---|---|---|---|---|---|---|---|---|---|
ALL | 327 | 104 | 17 | 17 | 3 | 81 | 6 | 16 | 2 |
AMP PEAK 2(2Q33.1) CNV | 55 | 18 | 9 | 4 | 0 | 25 | 2 | 8 | 1 |
AMP PEAK 2(2Q33.1) WILD-TYPE | 272 | 86 | 8 | 13 | 3 | 56 | 4 | 8 | 1 |
P value = 0.000225 (Fisher's exact test), Q value = 0.18
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
AMP PEAK 6(7P21.3) CNV | 210 | 20 | 99 | 5 |
AMP PEAK 6(7P21.3) WILD-TYPE | 147 | 34 | 44 | 8 |
P value = 2.77e-05 (Chi-square test), Q value = 0.022
nPatients | N0 | N1 | N1A | N1B | N1C | N2 | N2A | N2B | NX |
---|---|---|---|---|---|---|---|---|---|
ALL | 327 | 104 | 17 | 17 | 3 | 81 | 6 | 16 | 2 |
AMP PEAK 11(10Q22.3) CNV | 12 | 7 | 1 | 1 | 2 | 12 | 0 | 0 | 0 |
AMP PEAK 11(10Q22.3) WILD-TYPE | 315 | 97 | 16 | 16 | 1 | 69 | 6 | 16 | 2 |
P value = 1.21e-09 (Fisher's exact test), Q value = 9.8e-07
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
AMP PEAK 14(13Q12.13) CNV | 233 | 16 | 112 | 5 |
AMP PEAK 14(13Q12.13) WILD-TYPE | 124 | 38 | 31 | 8 |
P value = 2.65e-09 (Fisher's exact test), Q value = 2.2e-06
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
AMP PEAK 15(13Q12.2) CNV | 229 | 16 | 111 | 5 |
AMP PEAK 15(13Q12.2) WILD-TYPE | 128 | 38 | 32 | 8 |
P value = 3.25e-08 (Fisher's exact test), Q value = 2.6e-05
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
AMP PEAK 16(13Q22.1) CNV | 235 | 18 | 109 | 4 |
AMP PEAK 16(13Q22.1) WILD-TYPE | 122 | 36 | 34 | 9 |
P value = 1.14e-05 (Fisher's exact test), Q value = 0.0092
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
AMP PEAK 24(20P11.21) CNV | 208 | 20 | 103 | 4 |
AMP PEAK 24(20P11.21) WILD-TYPE | 149 | 34 | 40 | 9 |
P value = 9.13e-06 (Fisher's exact test), Q value = 0.0074
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
AMP PEAK 25(20Q11.21) CNV | 295 | 141 |
AMP PEAK 25(20Q11.21) WILD-TYPE | 117 | 18 |
P value = 7.95e-12 (Fisher's exact test), Q value = 6.5e-09
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
AMP PEAK 25(20Q11.21) CNV | 270 | 24 | 132 | 7 |
AMP PEAK 25(20Q11.21) WILD-TYPE | 87 | 30 | 11 | 6 |
P value = 4.74e-06 (Fisher's exact test), Q value = 0.0038
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
AMP PEAK 26(20Q12) CNV | 296 | 142 |
AMP PEAK 26(20Q12) WILD-TYPE | 116 | 17 |
P value = 5.41e-13 (Fisher's exact test), Q value = 4.4e-10
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
AMP PEAK 26(20Q12) CNV | 272 | 23 | 133 | 7 |
AMP PEAK 26(20Q12) WILD-TYPE | 85 | 31 | 10 | 6 |
P value = 0.00019 (Chi-square test), Q value = 0.15
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 98 | 1 | 41 | 154 | 10 | 3 | 27 | 22 | 70 | 47 | 57 | 25 | 1 |
AMP PEAK 26(20Q12) CNV | 74 | 1 | 24 | 107 | 5 | 3 | 19 | 21 | 55 | 40 | 51 | 24 | 0 |
AMP PEAK 26(20Q12) WILD-TYPE | 24 | 0 | 17 | 47 | 5 | 0 | 8 | 1 | 15 | 7 | 6 | 1 | 1 |
P value = 2.18e-05 (Fisher's exact test), Q value = 0.018
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
AMP PEAK 27(20Q13.32) CNV | 299 | 141 |
AMP PEAK 27(20Q13.32) WILD-TYPE | 113 | 18 |
P value = 8.79e-12 (Fisher's exact test), Q value = 7.2e-09
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
AMP PEAK 27(20Q13.32) CNV | 274 | 24 | 132 | 7 |
AMP PEAK 27(20Q13.32) WILD-TYPE | 83 | 30 | 11 | 6 |
P value = 2.78e-05 (Fisher's exact test), Q value = 0.022
nPatients | NO | YES |
---|---|---|
ALL | 9 | 566 |
DEL PEAK 10(4P16.1) CNV | 9 | 173 |
DEL PEAK 10(4P16.1) WILD-TYPE | 0 | 393 |
P value = 2.4e-05 (Fisher's exact test), Q value = 0.019
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
DEL PEAK 18(8P23.2) CNV | 172 | 98 |
DEL PEAK 18(8P23.2) WILD-TYPE | 240 | 61 |
P value = 2.72e-05 (Fisher's exact test), Q value = 0.022
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
DEL PEAK 18(8P23.2) CNV | 156 | 15 | 89 | 7 |
DEL PEAK 18(8P23.2) WILD-TYPE | 201 | 39 | 54 | 6 |
P value = 0.000164 (Chi-square test), Q value = 0.13
nPatients | N0 | N1 | N1A | N1B | N1C | N2 | N2A | N2B | NX |
---|---|---|---|---|---|---|---|---|---|
ALL | 327 | 104 | 17 | 17 | 3 | 81 | 6 | 16 | 2 |
DEL PEAK 18(8P23.2) CNV | 129 | 57 | 10 | 7 | 1 | 55 | 1 | 9 | 2 |
DEL PEAK 18(8P23.2) WILD-TYPE | 198 | 47 | 7 | 10 | 2 | 26 | 5 | 7 | 0 |
P value = 0.000245 (Fisher's exact test), Q value = 0.19
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
DEL PEAK 19(8P22) CNV | 168 | 16 | 89 | 7 |
DEL PEAK 19(8P22) WILD-TYPE | 189 | 38 | 54 | 6 |
P value = 1.79e-05 (Chi-square test), Q value = 0.014
nPatients | N0 | N1 | N1A | N1B | N1C | N2 | N2A | N2B | NX |
---|---|---|---|---|---|---|---|---|---|
ALL | 327 | 104 | 17 | 17 | 3 | 81 | 6 | 16 | 2 |
DEL PEAK 19(8P22) CNV | 133 | 60 | 11 | 7 | 1 | 59 | 2 | 9 | 2 |
DEL PEAK 19(8P22) WILD-TYPE | 194 | 44 | 6 | 10 | 2 | 22 | 4 | 7 | 0 |
P value = 0.000114 (t-test), Q value = 0.091
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 2.2 (4.7) |
DEL PEAK 19(8P22) CNV | 273 | 3.0 (5.7) |
DEL PEAK 19(8P22) WILD-TYPE | 268 | 1.4 (3.3) |
P value = 1.15e-06 (Fisher's exact test), Q value = 0.00093
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
DEL PEAK 30(14Q22.1) CNV | 115 | 4 | 62 | 1 |
DEL PEAK 30(14Q22.1) WILD-TYPE | 242 | 50 | 81 | 12 |
P value = 8.33e-05 (logrank test), Q value = 0.067
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 451 | 60 | 0.1 - 135.5 (7.0) |
DEL PEAK 34(16P13.3) CNV | 43 | 13 | 0.2 - 49.9 (8.2) |
DEL PEAK 34(16P13.3) WILD-TYPE | 408 | 47 | 0.1 - 135.5 (7.0) |
P value = 6.55e-08 (Fisher's exact test), Q value = 5.3e-05
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
DEL PEAK 36(17P12) CNV | 213 | 14 | 103 | 6 |
DEL PEAK 36(17P12) WILD-TYPE | 144 | 40 | 40 | 7 |
P value = 1.82e-06 (Fisher's exact test), Q value = 0.0015
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
DEL PEAK 38(18P11.31) CNV | 219 | 119 |
DEL PEAK 38(18P11.31) WILD-TYPE | 193 | 40 |
P value = 1.52e-16 (Fisher's exact test), Q value = 1.2e-13
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
DEL PEAK 38(18P11.31) CNV | 211 | 7 | 113 | 6 |
DEL PEAK 38(18P11.31) WILD-TYPE | 146 | 47 | 30 | 7 |
P value = 1.57e-09 (Fisher's exact test), Q value = 1.3e-06
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
DEL PEAK 39(18Q12.2) CNV | 247 | 136 |
DEL PEAK 39(18Q12.2) WILD-TYPE | 165 | 23 |
P value = 8.26e-18 (Fisher's exact test), Q value = 6.8e-15
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
DEL PEAK 39(18Q12.2) CNV | 235 | 11 | 125 | 10 |
DEL PEAK 39(18Q12.2) WILD-TYPE | 122 | 43 | 18 | 3 |
P value = 1.07e-09 (Fisher's exact test), Q value = 8.7e-07
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
DEL PEAK 40(18Q21.2) CNV | 260 | 140 |
DEL PEAK 40(18Q21.2) WILD-TYPE | 152 | 19 |
P value = 3.54e-16 (Fisher's exact test), Q value = 2.9e-13
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
DEL PEAK 40(18Q21.2) CNV | 245 | 14 | 126 | 12 |
DEL PEAK 40(18Q21.2) WILD-TYPE | 112 | 40 | 17 | 1 |
P value = 0.000227 (Chi-square test), Q value = 0.18
nPatients | N0 | N1 | N1A | N1B | N1C | N2 | N2A | N2B | NX |
---|---|---|---|---|---|---|---|---|---|
ALL | 327 | 104 | 17 | 17 | 3 | 81 | 6 | 16 | 2 |
DEL PEAK 40(18Q21.2) CNV | 201 | 85 | 11 | 13 | 3 | 68 | 5 | 13 | 2 |
DEL PEAK 40(18Q21.2) WILD-TYPE | 126 | 19 | 6 | 4 | 0 | 13 | 1 | 3 | 0 |
P value = 4.49e-05 (Chi-square test), Q value = 0.036
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 98 | 1 | 41 | 154 | 10 | 3 | 27 | 22 | 70 | 47 | 57 | 25 | 1 |
DEL PEAK 40(18Q21.2) CNV | 58 | 0 | 25 | 96 | 4 | 3 | 17 | 18 | 54 | 39 | 51 | 22 | 1 |
DEL PEAK 40(18Q21.2) WILD-TYPE | 40 | 1 | 16 | 58 | 6 | 0 | 10 | 4 | 16 | 8 | 6 | 3 | 0 |
P value = 1.94e-07 (Fisher's exact test), Q value = 0.00016
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
DEL PEAK 41(18Q22.1) CNV | 260 | 135 |
DEL PEAK 41(18Q22.1) WILD-TYPE | 152 | 24 |
P value = 2.05e-15 (Fisher's exact test), Q value = 1.7e-12
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 357 | 54 | 143 | 13 |
DEL PEAK 41(18Q22.1) CNV | 246 | 13 | 124 | 10 |
DEL PEAK 41(18Q22.1) WILD-TYPE | 111 | 41 | 19 | 3 |
P value = 0.000104 (Chi-square test), Q value = 0.083
nPatients | STAGE I | STAGE IA | STAGE II | STAGE IIA | STAGE IIB | STAGE IIC | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE IVA | STAGE IVB |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 98 | 1 | 41 | 154 | 10 | 3 | 27 | 22 | 70 | 47 | 57 | 25 | 1 |
DEL PEAK 41(18Q22.1) CNV | 58 | 0 | 25 | 96 | 4 | 3 | 15 | 17 | 53 | 39 | 50 | 22 | 1 |
DEL PEAK 41(18Q22.1) WILD-TYPE | 40 | 1 | 16 | 58 | 6 | 0 | 12 | 5 | 17 | 8 | 7 | 3 | 0 |
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Mutation data file = all_lesions.conf_99.cnv.cluster.txt
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Clinical data file = COADREAD-TP.clin.merged.picked.txt
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Number of patients = 575
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Number of significantly arm-level cnvs = 75
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Number of selected clinical features = 12
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Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
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 mutations 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.