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, 53 significant findings detected with Q value < 0.25.
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Amp Peak 5(6p21.1) cnv correlated to 'PATHOLOGY.N'.
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Amp Peak 6(7p21.3) cnv correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Amp Peak 14(13q12.13) cnv correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Amp Peak 15(13q12.2) cnv correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Amp Peak 16(13q22.1) cnv correlated to 'HISTOLOGICAL.TYPE' and 'PATHOLOGY.N'.
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Amp Peak 18(16p11.2) cnv correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
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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', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
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Amp Peak 26(20q12) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
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Amp Peak 27(20q13.32) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
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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', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Del Peak 19(8p22) cnv correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', 'TUMOR.STAGE', 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', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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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', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Del Peak 40(18q21.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Del Peak 41(18q22.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Del Peak 42(19p13.3) cnv correlated to 'PATHOLOGY.N'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 75 arm-level results and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 53 significant findings detected.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
GENDER |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | |
Del Peak 18(8p23 2) | 0 (0%) | 303 |
0.619 (1.00) |
0.205 (1.00) |
2.4e-05 (0.0209) |
0.18 (1.00) |
2.9e-05 (0.0252) |
0.081 (1.00) |
2.78e-05 (0.0242) |
0.00989 (1.00) |
3.4e-05 (0.0294) |
0.0155 (1.00) |
0.00536 (1.00) |
0.000422 (0.356) |
Del Peak 19(8p22) | 0 (0%) | 290 |
0.597 (1.00) |
0.317 (1.00) |
0.000379 (0.321) |
0.403 (1.00) |
0.000256 (0.217) |
0.0753 (1.00) |
1.97e-06 (0.00173) |
0.00381 (1.00) |
1.24e-06 (0.0011) |
0.0196 (1.00) |
0.00797 (1.00) |
0.000106 (0.0907) |
Del Peak 39(18q12 2) | 0 (0%) | 189 |
0.942 (1.00) |
0.0817 (1.00) |
1.57e-09 (1.4e-06) |
0.477 (1.00) |
8.59e-18 (7.73e-15) |
0.421 (1.00) |
0.000131 (0.112) |
0.00447 (1.00) |
6.82e-05 (0.0587) |
0.034 (1.00) |
0.0373 (1.00) |
0.00847 (1.00) |
Del Peak 40(18q21 2) | 0 (0%) | 172 |
0.481 (1.00) |
0.0823 (1.00) |
1.07e-09 (9.55e-07) |
0.145 (1.00) |
3.7e-16 (3.32e-13) |
0.315 (1.00) |
1.95e-06 (0.00172) |
0.00162 (1.00) |
4.1e-07 (0.000363) |
0.0637 (1.00) |
0.0438 (1.00) |
0.000978 (0.811) |
Del Peak 41(18q22 1) | 0 (0%) | 177 |
0.332 (1.00) |
0.221 (1.00) |
1.94e-07 (0.000172) |
0.239 (1.00) |
2.07e-15 (1.86e-12) |
0.444 (1.00) |
1.14e-05 (0.01) |
0.00238 (1.00) |
4.68e-06 (0.00411) |
0.0632 (1.00) |
0.0824 (1.00) |
0.00182 (1.00) |
Amp Peak 6(7p21 3) | 0 (0%) | 238 |
0.304 (1.00) |
0.103 (1.00) |
0.0292 (1.00) |
0.734 (1.00) |
0.000225 (0.191) |
0.889 (1.00) |
1.23e-05 (0.0107) |
0.0274 (1.00) |
4.42e-06 (0.00389) |
0.0882 (1.00) |
0.0892 (1.00) |
0.0339 (1.00) |
Amp Peak 14(13q12 13) | 0 (0%) | 204 |
0.126 (1.00) |
0.314 (1.00) |
0.00246 (1.00) |
0.727 (1.00) |
1.18e-09 (1.05e-06) |
0.561 (1.00) |
3.88e-05 (0.0336) |
0.0101 (1.00) |
7.49e-05 (0.0644) |
1 (1.00) |
0.0288 (1.00) |
0.0342 (1.00) |
Amp Peak 15(13q12 2) | 0 (0%) | 209 |
0.101 (1.00) |
0.239 (1.00) |
0.00188 (1.00) |
0.543 (1.00) |
2.61e-09 (2.32e-06) |
0.533 (1.00) |
9.03e-05 (0.0774) |
0.023 (1.00) |
0.000184 (0.156) |
1 (1.00) |
0.051 (1.00) |
0.0355 (1.00) |
Amp Peak 25(20q11 21) | 0 (0%) | 136 |
0.317 (1.00) |
0.823 (1.00) |
9.13e-06 (0.008) |
0.376 (1.00) |
7.88e-12 (7.05e-09) |
0.506 (1.00) |
0.00141 (1.00) |
0.00533 (1.00) |
0.000107 (0.0916) |
0.693 (1.00) |
0.0588 (1.00) |
0.344 (1.00) |
Amp Peak 26(20q12) | 0 (0%) | 134 |
0.274 (1.00) |
0.726 (1.00) |
4.74e-06 (0.00416) |
0.374 (1.00) |
5.38e-13 (4.82e-10) |
0.611 (1.00) |
0.00101 (0.84) |
0.00129 (1.00) |
4.17e-05 (0.036) |
0.692 (1.00) |
0.059 (1.00) |
0.393 (1.00) |
Amp Peak 27(20q13 32) | 0 (0%) | 131 |
0.369 (1.00) |
0.658 (1.00) |
2.18e-05 (0.019) |
0.551 (1.00) |
8.76e-12 (7.83e-09) |
0.588 (1.00) |
0.00158 (1.00) |
0.00424 (1.00) |
0.000131 (0.112) |
0.692 (1.00) |
0.0589 (1.00) |
0.246 (1.00) |
Del Peak 36(17p12) | 0 (0%) | 232 |
0.656 (1.00) |
0.0983 (1.00) |
0.00169 (1.00) |
0.609 (1.00) |
6.48e-08 (5.75e-05) |
0.419 (1.00) |
0.000121 (0.104) |
0.041 (1.00) |
3.15e-05 (0.0273) |
0.325 (1.00) |
0.119 (1.00) |
0.00223 (1.00) |
Amp Peak 16(13q22 1) | 0 (0%) | 204 |
0.0454 (1.00) |
0.444 (1.00) |
0.0249 (1.00) |
0.221 (1.00) |
3.13e-08 (2.78e-05) |
0.736 (1.00) |
0.000127 (0.108) |
0.024 (1.00) |
0.0006 (0.504) |
0.503 (1.00) |
0.162 (1.00) |
0.185 (1.00) |
Amp Peak 18(16p11 2) | 0 (0%) | 414 |
0.838 (1.00) |
0.26 (1.00) |
0.918 (1.00) |
0.71 (1.00) |
0.0024 (1.00) |
0.721 (1.00) |
5.82e-05 (0.0502) |
0.111 (1.00) |
8.54e-05 (0.0733) |
0.715 (1.00) |
0.394 (1.00) |
0.0175 (1.00) |
Del Peak 38(18p11 31) | 0 (0%) | 234 |
0.98 (1.00) |
0.059 (1.00) |
1.82e-06 (0.00161) |
1 (1.00) |
1.53e-16 (1.37e-13) |
0.882 (1.00) |
0.0106 (1.00) |
0.000584 (0.492) |
0.000895 (0.743) |
0.322 (1.00) |
0.024 (1.00) |
0.457 (1.00) |
Amp Peak 5(6p21 1) | 0 (0%) | 429 |
0.489 (1.00) |
0.682 (1.00) |
0.0314 (1.00) |
0.15 (1.00) |
0.00236 (1.00) |
0.215 (1.00) |
3.17e-05 (0.0275) |
0.109 (1.00) |
0.000331 (0.28) |
0.00136 (1.00) |
0.145 (1.00) |
0.00273 (1.00) |
Amp Peak 24(20p11 21) | 0 (0%) | 236 |
0.808 (1.00) |
0.709 (1.00) |
0.00784 (1.00) |
0.0413 (1.00) |
1.12e-05 (0.00984) |
0.885 (1.00) |
0.382 (1.00) |
0.00312 (1.00) |
0.0516 (1.00) |
0.32 (1.00) |
0.696 (1.00) |
0.93 (1.00) |
Del Peak 10(4p16 1) | 0 (0%) | 393 |
0.0406 (1.00) |
0.954 (1.00) |
0.0561 (1.00) |
0.128 (1.00) |
0.0277 (1.00) |
0.985 (1.00) |
0.00057 (0.48) |
0.0131 (1.00) |
0.00164 (1.00) |
2.78e-05 (0.0242) |
0.0821 (1.00) |
0.0016 (1.00) |
Del Peak 30(14q22 1) | 0 (0%) | 390 |
0.208 (1.00) |
0.233 (1.00) |
0.0212 (1.00) |
0.421 (1.00) |
1.15e-06 (0.00101) |
0.78 (1.00) |
0.00362 (1.00) |
0.145 (1.00) |
0.175 (1.00) |
0.725 (1.00) |
0.539 (1.00) |
0.691 (1.00) |
Del Peak 34(16p13 3) | 0 (0%) | 517 |
4.34e-05 (0.0375) |
0.254 (1.00) |
0.359 (1.00) |
0.89 (1.00) |
0.418 (1.00) |
0.0689 (1.00) |
0.132 (1.00) |
0.381 (1.00) |
0.101 (1.00) |
0.609 (1.00) |
0.749 (1.00) |
0.0606 (1.00) |
Del Peak 42(19p13 3) | 0 (0%) | 483 |
0.406 (1.00) |
0.183 (1.00) |
0.0305 (1.00) |
0.733 (1.00) |
0.0678 (1.00) |
0.407 (1.00) |
7.64e-05 (0.0656) |
0.0275 (1.00) |
0.00312 (1.00) |
0.641 (1.00) |
0.13 (1.00) |
0.0025 (1.00) |
Amp Peak 1(1q31 1) | 0 (0%) | 441 |
0.466 (1.00) |
0.292 (1.00) |
0.0268 (1.00) |
0.236 (1.00) |
0.0946 (1.00) |
0.381 (1.00) |
0.0539 (1.00) |
0.175 (1.00) |
0.0343 (1.00) |
0.0357 (1.00) |
0.503 (1.00) |
0.0152 (1.00) |
Amp Peak 2(2q33 1) | 0 (0%) | 452 |
0.135 (1.00) |
0.385 (1.00) |
0.031 (1.00) |
1 (1.00) |
0.00379 (1.00) |
0.686 (1.00) |
0.00128 (1.00) |
0.541 (1.00) |
0.0227 (1.00) |
0.103 (1.00) |
0.516 (1.00) |
0.0246 (1.00) |
Amp Peak 3(5p12) | 0 (0%) | 468 |
0.0162 (1.00) |
0.372 (1.00) |
0.151 (1.00) |
0.748 (1.00) |
0.0568 (1.00) |
0.396 (1.00) |
0.0431 (1.00) |
0.354 (1.00) |
0.191 (1.00) |
0.379 (1.00) |
0.0289 (1.00) |
0.0708 (1.00) |
Amp Peak 4(5q22 3) | 0 (0%) | 516 |
0.75 (1.00) |
0.865 (1.00) |
0.445 (1.00) |
0.891 (1.00) |
0.316 (1.00) |
0.907 (1.00) |
0.176 (1.00) |
0.032 (1.00) |
0.12 (1.00) |
1 (1.00) |
0.0798 (1.00) |
0.492 (1.00) |
Amp Peak 7(8p11 23) | 0 (0%) | 379 |
0.472 (1.00) |
0.752 (1.00) |
0.625 (1.00) |
0.482 (1.00) |
0.232 (1.00) |
0.409 (1.00) |
0.503 (1.00) |
0.413 (1.00) |
0.88 (1.00) |
0.498 (1.00) |
0.175 (1.00) |
0.633 (1.00) |
Amp Peak 8(8p11 21) | 0 (0%) | 337 |
0.633 (1.00) |
0.597 (1.00) |
0.636 (1.00) |
0.204 (1.00) |
0.12 (1.00) |
0.5 (1.00) |
0.333 (1.00) |
0.305 (1.00) |
0.475 (1.00) |
0.742 (1.00) |
0.0277 (1.00) |
0.409 (1.00) |
Amp Peak 9(8q12 1) | 0 (0%) | 266 |
0.907 (1.00) |
0.19 (1.00) |
0.303 (1.00) |
0.615 (1.00) |
0.0093 (1.00) |
0.128 (1.00) |
0.0853 (1.00) |
0.0256 (1.00) |
0.0726 (1.00) |
0.0423 (1.00) |
0.0328 (1.00) |
0.027 (1.00) |
Amp Peak 10(8q24 21) | 0 (0%) | 230 |
0.545 (1.00) |
0.236 (1.00) |
0.0863 (1.00) |
0.394 (1.00) |
0.0113 (1.00) |
0.143 (1.00) |
0.171 (1.00) |
0.0551 (1.00) |
0.233 (1.00) |
0.0931 (1.00) |
0.0997 (1.00) |
0.0585 (1.00) |
Amp Peak 11(10q22 3) | 0 (0%) | 540 |
0.819 (1.00) |
0.303 (1.00) |
1 (1.00) |
0.487 (1.00) |
0.932 (1.00) |
0.141 (1.00) |
0.00814 (1.00) |
0.912 (1.00) |
0.116 (1.00) |
0.434 (1.00) |
0.91 (1.00) |
0.0883 (1.00) |
Amp Peak 12(11p15 5) | 0 (0%) | 446 |
0.709 (1.00) |
0.0608 (1.00) |
0.145 (1.00) |
0.549 (1.00) |
0.00144 (1.00) |
0.293 (1.00) |
0.712 (1.00) |
0.385 (1.00) |
0.808 (1.00) |
0.12 (1.00) |
0.706 (1.00) |
0.42 (1.00) |
Amp Peak 13(12p13 32) | 0 (0%) | 431 |
0.26 (1.00) |
0.0696 (1.00) |
0.829 (1.00) |
0.5 (1.00) |
0.351 (1.00) |
0.387 (1.00) |
0.0536 (1.00) |
0.0859 (1.00) |
0.0625 (1.00) |
0.698 (1.00) |
0.612 (1.00) |
0.442 (1.00) |
Amp Peak 17(15q26 1) | 0 (0%) | 532 |
0.0824 (1.00) |
0.753 (1.00) |
0.291 (1.00) |
0.0582 (1.00) |
0.433 (1.00) |
0.287 (1.00) |
0.00409 (1.00) |
0.649 (1.00) |
0.198 (1.00) |
0.141 (1.00) |
0.38 (1.00) |
0.0562 (1.00) |
Amp Peak 19(17q12) | 0 (0%) | 431 |
0.489 (1.00) |
0.363 (1.00) |
0.591 (1.00) |
0.101 (1.00) |
0.457 (1.00) |
0.417 (1.00) |
0.152 (1.00) |
0.0117 (1.00) |
0.0158 (1.00) |
0.462 (1.00) |
0.0311 (1.00) |
0.345 (1.00) |
Amp Peak 20(17q24 1) | 0 (0%) | 447 |
0.0431 (1.00) |
0.245 (1.00) |
0.911 (1.00) |
0.617 (1.00) |
0.0878 (1.00) |
0.771 (1.00) |
0.886 (1.00) |
0.0549 (1.00) |
0.219 (1.00) |
0.691 (1.00) |
0.0941 (1.00) |
0.689 (1.00) |
Amp Peak 21(19p13 2) | 0 (0%) | 478 |
0.144 (1.00) |
0.493 (1.00) |
0.216 (1.00) |
0.182 (1.00) |
0.0516 (1.00) |
0.409 (1.00) |
0.0339 (1.00) |
0.233 (1.00) |
0.126 (1.00) |
1 (1.00) |
0.184 (1.00) |
0.972 (1.00) |
Amp Peak 22(19q12) | 0 (0%) | 453 |
0.628 (1.00) |
0.941 (1.00) |
0.256 (1.00) |
0.185 (1.00) |
0.0293 (1.00) |
0.654 (1.00) |
0.0943 (1.00) |
0.139 (1.00) |
0.226 (1.00) |
0.692 (1.00) |
0.592 (1.00) |
0.419 (1.00) |
Amp Peak 23(20p11 23) | 0 (0%) | 274 |
0.699 (1.00) |
0.921 (1.00) |
0.0194 (1.00) |
0.0364 (1.00) |
0.00072 (0.601) |
0.873 (1.00) |
0.0368 (1.00) |
0.00134 (1.00) |
0.011 (1.00) |
0.181 (1.00) |
0.383 (1.00) |
0.305 (1.00) |
Amp Peak 28(Xq28) | 0 (0%) | 454 |
0.245 (1.00) |
0.209 (1.00) |
0.421 (1.00) |
0.838 (1.00) |
0.0249 (1.00) |
0.521 (1.00) |
0.017 (1.00) |
0.219 (1.00) |
0.0635 (1.00) |
0.693 (1.00) |
0.29 (1.00) |
0.286 (1.00) |
Del Peak 1(1p36 11) | 0 (0%) | 353 |
0.051 (1.00) |
0.105 (1.00) |
0.126 (1.00) |
0.392 (1.00) |
0.00644 (1.00) |
0.238 (1.00) |
0.000887 (0.737) |
0.000615 (0.516) |
0.000734 (0.611) |
0.739 (1.00) |
0.0585 (1.00) |
0.000594 (0.5) |
Del Peak 2(1p33) | 0 (0%) | 419 |
0.0178 (1.00) |
0.836 (1.00) |
0.401 (1.00) |
0.851 (1.00) |
0.0797 (1.00) |
0.226 (1.00) |
0.00507 (1.00) |
0.0106 (1.00) |
0.0159 (1.00) |
0.709 (1.00) |
0.138 (1.00) |
0.0154 (1.00) |
Del Peak 3(1p13 2) | 0 (0%) | 418 |
0.0696 (1.00) |
0.841 (1.00) |
0.248 (1.00) |
0.639 (1.00) |
0.135 (1.00) |
0.15 (1.00) |
0.00213 (1.00) |
0.00127 (1.00) |
0.0162 (1.00) |
0.265 (1.00) |
0.205 (1.00) |
0.00297 (1.00) |
Del Peak 4(2p12) | 0 (0%) | 555 |
0.796 (1.00) |
0.179 (1.00) |
0.00346 (1.00) |
0.821 (1.00) |
0.0208 (1.00) |
1 (1.00) |
0.351 (1.00) |
0.56 (1.00) |
0.329 (1.00) |
0.275 (1.00) |
0.876 (1.00) |
0.318 (1.00) |
Del Peak 5(2q22 1) | 0 (0%) | 542 |
0.85 (1.00) |
0.564 (1.00) |
0.842 (1.00) |
0.474 (1.00) |
0.927 (1.00) |
0.669 (1.00) |
0.609 (1.00) |
0.689 (1.00) |
0.174 (1.00) |
1 (1.00) |
1 (1.00) |
0.894 (1.00) |
Del Peak 6(2q37 2) | 0 (0%) | 545 |
0.842 (1.00) |
0.139 (1.00) |
0.835 (1.00) |
0.458 (1.00) |
0.945 (1.00) |
0.344 (1.00) |
0.208 (1.00) |
0.133 (1.00) |
0.0449 (1.00) |
1 (1.00) |
1 (1.00) |
0.859 (1.00) |
Del Peak 7(3p26 3) | 0 (0%) | 491 |
0.000643 (0.538) |
0.855 (1.00) |
0.691 (1.00) |
0.723 (1.00) |
0.19 (1.00) |
0.0373 (1.00) |
0.0192 (1.00) |
0.00105 (0.865) |
0.000684 (0.571) |
0.131 (1.00) |
0.0674 (1.00) |
0.0296 (1.00) |
Del Peak 8(3p14 2) | 0 (0%) | 471 |
0.216 (1.00) |
0.578 (1.00) |
0.808 (1.00) |
0.664 (1.00) |
0.416 (1.00) |
0.136 (1.00) |
0.181 (1.00) |
0.0317 (1.00) |
0.0461 (1.00) |
0.669 (1.00) |
0.123 (1.00) |
0.0236 (1.00) |
Del Peak 9(3q26 31) | 0 (0%) | 519 |
0.714 (1.00) |
0.996 (1.00) |
0.874 (1.00) |
0.0931 (1.00) |
0.0423 (1.00) |
0.0139 (1.00) |
0.371 (1.00) |
0.327 (1.00) |
0.00215 (1.00) |
0.216 (1.00) |
0.111 (1.00) |
0.504 (1.00) |
Del Peak 11(4q22 1) | 0 (0%) | 377 |
0.193 (1.00) |
0.42 (1.00) |
0.00417 (1.00) |
0.187 (1.00) |
0.00142 (1.00) |
0.134 (1.00) |
0.0018 (1.00) |
0.369 (1.00) |
0.0375 (1.00) |
0.00114 (0.937) |
0.426 (1.00) |
0.00264 (1.00) |
Del Peak 12(4q35 1) | 0 (0%) | 364 |
0.277 (1.00) |
0.303 (1.00) |
0.0325 (1.00) |
0.863 (1.00) |
0.021 (1.00) |
0.702 (1.00) |
0.00325 (1.00) |
0.645 (1.00) |
0.118 (1.00) |
0.00185 (1.00) |
0.788 (1.00) |
0.0218 (1.00) |
Del Peak 13(5q11 2) | 0 (0%) | 435 |
0.164 (1.00) |
0.0866 (1.00) |
0.0389 (1.00) |
1 (1.00) |
0.0275 (1.00) |
0.976 (1.00) |
0.0078 (1.00) |
0.0232 (1.00) |
0.0344 (1.00) |
0.00103 (0.851) |
0.271 (1.00) |
0.0226 (1.00) |
Del Peak 14(5q22 2) | 0 (0%) | 403 |
0.0866 (1.00) |
0.359 (1.00) |
0.155 (1.00) |
0.648 (1.00) |
0.0624 (1.00) |
0.773 (1.00) |
0.0168 (1.00) |
0.0311 (1.00) |
0.0332 (1.00) |
0.000382 (0.322) |
0.103 (1.00) |
0.145 (1.00) |
Del Peak 15(6p25 3) | 0 (0%) | 497 |
0.611 (1.00) |
0.0683 (1.00) |
1 (1.00) |
0.0876 (1.00) |
0.544 (1.00) |
0.261 (1.00) |
0.534 (1.00) |
0.326 (1.00) |
0.223 (1.00) |
0.351 (1.00) |
0.324 (1.00) |
0.749 (1.00) |
Del Peak 16(6q26) | 0 (0%) | 485 |
0.029 (1.00) |
0.9 (1.00) |
0.368 (1.00) |
0.301 (1.00) |
0.0485 (1.00) |
0.0584 (1.00) |
0.0136 (1.00) |
0.0389 (1.00) |
0.594 (1.00) |
0.637 (1.00) |
0.0625 (1.00) |
0.00961 (1.00) |
Del Peak 17(7q31 1) | 0 (0%) | 560 |
1 (1.00) |
0.329 (1.00) |
1 (1.00) |
0.307 (1.00) |
0.503 (1.00) |
0.525 (1.00) |
0.673 (1.00) |
0.33 (1.00) |
0.342 (1.00) |
1 (1.00) |
0.706 (1.00) |
0.61 (1.00) |
Del Peak 20(8p11 21) | 0 (0%) | 451 |
0.598 (1.00) |
0.329 (1.00) |
0.031 (1.00) |
0.542 (1.00) |
0.167 (1.00) |
0.535 (1.00) |
0.00723 (1.00) |
0.0823 (1.00) |
0.027 (1.00) |
0.414 (1.00) |
0.0885 (1.00) |
0.0888 (1.00) |
Del Peak 21(8q11 1) | 0 (0%) | 531 |
0.889 (1.00) |
0.382 (1.00) |
0.16 (1.00) |
0.208 (1.00) |
0.418 (1.00) |
0.714 (1.00) |
0.0274 (1.00) |
0.00202 (1.00) |
0.0962 (1.00) |
0.514 (1.00) |
0.418 (1.00) |
0.302 (1.00) |
Del Peak 22(9p24 2) | 0 (0%) | 497 |
0.00207 (1.00) |
0.12 (1.00) |
0.496 (1.00) |
0.0507 (1.00) |
0.452 (1.00) |
0.497 (1.00) |
0.136 (1.00) |
0.0231 (1.00) |
0.291 (1.00) |
0.351 (1.00) |
0.0396 (1.00) |
0.237 (1.00) |
Del Peak 23(10p15 3) | 0 (0%) | 473 |
0.577 (1.00) |
0.0282 (1.00) |
0.271 (1.00) |
0.913 (1.00) |
0.364 (1.00) |
0.721 (1.00) |
0.00713 (1.00) |
0.181 (1.00) |
0.00847 (1.00) |
0.00145 (1.00) |
1 (1.00) |
0.0465 (1.00) |
Del Peak 24(10q21 1) | 0 (0%) | 457 |
0.869 (1.00) |
0.0152 (1.00) |
0.421 (1.00) |
0.535 (1.00) |
0.118 (1.00) |
0.723 (1.00) |
0.164 (1.00) |
0.682 (1.00) |
0.368 (1.00) |
0.00326 (1.00) |
0.167 (1.00) |
0.17 (1.00) |
Del Peak 25(10q23 31) | 0 (0%) | 430 |
0.566 (1.00) |
0.00668 (1.00) |
0.0408 (1.00) |
0.923 (1.00) |
0.0208 (1.00) |
0.206 (1.00) |
0.0139 (1.00) |
0.0621 (1.00) |
0.0977 (1.00) |
0.0013 (1.00) |
0.431 (1.00) |
0.201 (1.00) |
Del Peak 26(10q25 2) | 0 (0%) | 435 |
0.756 (1.00) |
0.0715 (1.00) |
0.128 (1.00) |
0.846 (1.00) |
0.0324 (1.00) |
0.218 (1.00) |
0.0134 (1.00) |
0.43 (1.00) |
0.116 (1.00) |
0.00103 (0.851) |
0.396 (1.00) |
0.172 (1.00) |
Del Peak 27(11q22 3) | 0 (0%) | 471 |
0.473 (1.00) |
0.396 (1.00) |
0.086 (1.00) |
0.588 (1.00) |
0.0532 (1.00) |
0.39 (1.00) |
0.0514 (1.00) |
0.633 (1.00) |
0.0927 (1.00) |
0.061 (1.00) |
0.63 (1.00) |
0.0422 (1.00) |
Del Peak 28(12p13 1) | 0 (0%) | 498 |
0.466 (1.00) |
0.472 (1.00) |
0.0256 (1.00) |
0.327 (1.00) |
0.000677 (0.566) |
0.501 (1.00) |
0.0319 (1.00) |
0.1 (1.00) |
0.208 (1.00) |
0.344 (1.00) |
0.557 (1.00) |
0.957 (1.00) |
Del Peak 29(12q21 2) | 0 (0%) | 495 |
0.636 (1.00) |
0.709 (1.00) |
0.0779 (1.00) |
0.717 (1.00) |
0.00837 (1.00) |
0.675 (1.00) |
0.0185 (1.00) |
0.0916 (1.00) |
0.239 (1.00) |
0.117 (1.00) |
1 (1.00) |
0.0773 (1.00) |
Del Peak 31(15q11 2) | 0 (0%) | 342 |
0.771 (1.00) |
0.618 (1.00) |
0.216 (1.00) |
0.496 (1.00) |
0.0549 (1.00) |
0.804 (1.00) |
0.0148 (1.00) |
0.264 (1.00) |
0.0414 (1.00) |
0.035 (1.00) |
0.68 (1.00) |
0.0616 (1.00) |
Del Peak 32(15q21 1) | 0 (0%) | 348 |
0.434 (1.00) |
0.603 (1.00) |
0.0355 (1.00) |
0.305 (1.00) |
0.0247 (1.00) |
0.846 (1.00) |
0.0271 (1.00) |
0.228 (1.00) |
0.125 (1.00) |
0.0327 (1.00) |
0.704 (1.00) |
0.0512 (1.00) |
Del Peak 33(15q22 33) | 0 (0%) | 358 |
0.555 (1.00) |
0.327 (1.00) |
0.012 (1.00) |
0.667 (1.00) |
0.00595 (1.00) |
0.0968 (1.00) |
0.00679 (1.00) |
0.211 (1.00) |
0.0235 (1.00) |
0.00229 (1.00) |
0.832 (1.00) |
0.0287 (1.00) |
Del Peak 35(16q23 1) | 0 (0%) | 503 |
0.0014 (1.00) |
0.264 (1.00) |
0.402 (1.00) |
0.167 (1.00) |
0.515 (1.00) |
0.252 (1.00) |
0.775 (1.00) |
0.951 (1.00) |
0.465 (1.00) |
1 (1.00) |
0.926 (1.00) |
0.239 (1.00) |
Del Peak 37(17q24 3) | 0 (0%) | 491 |
0.731 (1.00) |
0.305 (1.00) |
0.793 (1.00) |
0.0994 (1.00) |
0.99 (1.00) |
0.243 (1.00) |
0.0075 (1.00) |
0.352 (1.00) |
0.0357 (1.00) |
0.626 (1.00) |
0.324 (1.00) |
0.0455 (1.00) |
Del Peak 43(19q13 43) | 0 (0%) | 507 |
0.509 (1.00) |
0.816 (1.00) |
0.146 (1.00) |
0.3 (1.00) |
0.417 (1.00) |
0.44 (1.00) |
0.0156 (1.00) |
0.0712 (1.00) |
0.17 (1.00) |
0.289 (1.00) |
0.783 (1.00) |
0.0197 (1.00) |
Del Peak 44(20p12 1) | 0 (0%) | 396 |
0.108 (1.00) |
0.631 (1.00) |
0.0445 (1.00) |
0.321 (1.00) |
0.144 (1.00) |
0.468 (1.00) |
0.319 (1.00) |
0.827 (1.00) |
0.191 (1.00) |
0.0632 (1.00) |
0.405 (1.00) |
0.829 (1.00) |
Del Peak 45(20p12 1) | 0 (0%) | 396 |
0.108 (1.00) |
0.631 (1.00) |
0.0445 (1.00) |
0.321 (1.00) |
0.144 (1.00) |
0.468 (1.00) |
0.319 (1.00) |
0.827 (1.00) |
0.191 (1.00) |
0.0632 (1.00) |
0.405 (1.00) |
0.829 (1.00) |
Del Peak 46(21q11 2) | 0 (0%) | 380 |
0.515 (1.00) |
0.721 (1.00) |
0.00555 (1.00) |
0.66 (1.00) |
0.000632 (0.529) |
0.824 (1.00) |
0.0458 (1.00) |
0.614 (1.00) |
0.325 (1.00) |
0.175 (1.00) |
0.433 (1.00) |
0.00411 (1.00) |
Del Peak 47(22q13 32) | 0 (0%) | 371 |
0.04 (1.00) |
0.672 (1.00) |
0.173 (1.00) |
0.93 (1.00) |
0.00961 (1.00) |
0.45 (1.00) |
0.000791 (0.658) |
0.0275 (1.00) |
0.00938 (1.00) |
0.727 (1.00) |
0.293 (1.00) |
0.0122 (1.00) |
P value = 3.17e-05 (Fisher's exact test), Q value = 0.028
Table S1. Gene #5: 'Amp Peak 5(6p21.1)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
AMP PEAK 5(6P21.1) CNV | 63 | 39 | 43 |
AMP PEAK 5(6P21.1) WILD-TYPE | 265 | 101 | 60 |
Figure S1. Get High-res Image Gene #5: 'Amp Peak 5(6p21.1)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D5V7.png)
P value = 0.000225 (Fisher's exact test), Q value = 0.19
Table S2. Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
AMP PEAK 6(7P21.3) CNV | 210 | 20 | 99 | 5 |
AMP PEAK 6(7P21.3) WILD-TYPE | 146 | 34 | 44 | 8 |
Figure S2. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D6V5.png)
P value = 1.23e-05 (Fisher's exact test), Q value = 0.011
Table S3. Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
AMP PEAK 6(7P21.3) CNV | 164 | 100 | 69 |
AMP PEAK 6(7P21.3) WILD-TYPE | 164 | 40 | 34 |
Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D6V7.png)
P value = 4.42e-06 (Fisher's exact test), Q value = 0.0039
Table S4. Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
AMP PEAK 6(7P21.3) CNV | 54 | 93 | 114 | 57 |
AMP PEAK 6(7P21.3) WILD-TYPE | 43 | 114 | 52 | 24 |
Figure S4. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D6V9.png)
P value = 1.18e-09 (Fisher's exact test), Q value = 1.1e-06
Table S5. Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
AMP PEAK 14(13Q12.13) CNV | 233 | 16 | 112 | 5 |
AMP PEAK 14(13Q12.13) WILD-TYPE | 123 | 38 | 31 | 8 |
Figure S5. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D14V5.png)
P value = 3.88e-05 (Fisher's exact test), Q value = 0.034
Table S6. Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
AMP PEAK 14(13Q12.13) CNV | 186 | 105 | 77 |
AMP PEAK 14(13Q12.13) WILD-TYPE | 142 | 35 | 26 |
Figure S6. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D14V7.png)
P value = 7.49e-05 (Fisher's exact test), Q value = 0.064
Table S7. Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
AMP PEAK 14(13Q12.13) CNV | 60 | 112 | 117 | 65 |
AMP PEAK 14(13Q12.13) WILD-TYPE | 37 | 95 | 49 | 16 |
Figure S7. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D14V9.png)
P value = 2.61e-09 (Fisher's exact test), Q value = 2.3e-06
Table S8. Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
AMP PEAK 15(13Q12.2) CNV | 229 | 16 | 111 | 5 |
AMP PEAK 15(13Q12.2) WILD-TYPE | 127 | 38 | 32 | 8 |
Figure S8. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D15V5.png)
P value = 9.03e-05 (Fisher's exact test), Q value = 0.077
Table S9. Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
AMP PEAK 15(13Q12.2) CNV | 184 | 103 | 76 |
AMP PEAK 15(13Q12.2) WILD-TYPE | 144 | 37 | 27 |
Figure S9. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D15V7.png)
P value = 0.000184 (Fisher's exact test), Q value = 0.16
Table S10. Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
AMP PEAK 15(13Q12.2) CNV | 60 | 110 | 116 | 63 |
AMP PEAK 15(13Q12.2) WILD-TYPE | 37 | 97 | 50 | 18 |
Figure S10. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D15V9.png)
P value = 3.13e-08 (Fisher's exact test), Q value = 2.8e-05
Table S11. Gene #16: 'Amp Peak 16(13q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
AMP PEAK 16(13Q22.1) CNV | 235 | 18 | 109 | 4 |
AMP PEAK 16(13Q22.1) WILD-TYPE | 121 | 36 | 34 | 9 |
Figure S11. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D16V5.png)
P value = 0.000127 (Fisher's exact test), Q value = 0.11
Table S12. Gene #16: 'Amp Peak 16(13q22.1)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
AMP PEAK 16(13Q22.1) CNV | 187 | 105 | 75 |
AMP PEAK 16(13Q22.1) WILD-TYPE | 141 | 35 | 28 |
Figure S12. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D16V7.png)
P value = 5.82e-05 (Fisher's exact test), Q value = 0.05
Table S13. Gene #18: 'Amp Peak 18(16p11.2)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
AMP PEAK 18(16P11.2) CNV | 68 | 52 | 39 |
AMP PEAK 18(16P11.2) WILD-TYPE | 260 | 88 | 64 |
Figure S13. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D18V7.png)
P value = 8.54e-05 (Fisher's exact test), Q value = 0.073
Table S14. Gene #18: 'Amp Peak 18(16p11.2)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
AMP PEAK 18(16P11.2) CNV | 19 | 40 | 64 | 27 |
AMP PEAK 18(16P11.2) WILD-TYPE | 78 | 167 | 102 | 54 |
Figure S14. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D18V9.png)
P value = 1.12e-05 (Fisher's exact test), Q value = 0.0098
Table S15. Gene #24: 'Amp Peak 24(20p11.21)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
AMP PEAK 24(20P11.21) CNV | 207 | 20 | 103 | 4 |
AMP PEAK 24(20P11.21) WILD-TYPE | 149 | 34 | 40 | 9 |
Figure S15. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D24V5.png)
P value = 9.13e-06 (Fisher's exact test), Q value = 0.008
Table S16. Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
AMP PEAK 25(20Q11.21) CNV | 295 | 141 |
AMP PEAK 25(20Q11.21) WILD-TYPE | 117 | 18 |
Figure S16. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D25V3.png)
P value = 7.88e-12 (Fisher's exact test), Q value = 7.1e-09
Table S17. Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
AMP PEAK 25(20Q11.21) CNV | 269 | 24 | 132 | 7 |
AMP PEAK 25(20Q11.21) WILD-TYPE | 87 | 30 | 11 | 6 |
Figure S17. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D25V5.png)
P value = 0.000107 (Fisher's exact test), Q value = 0.092
Table S18. Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
AMP PEAK 25(20Q11.21) CNV | 74 | 136 | 136 | 71 |
AMP PEAK 25(20Q11.21) WILD-TYPE | 23 | 71 | 30 | 10 |
Figure S18. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D25V9.png)
P value = 4.74e-06 (Fisher's exact test), Q value = 0.0042
Table S19. Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
AMP PEAK 26(20Q12) CNV | 296 | 142 |
AMP PEAK 26(20Q12) WILD-TYPE | 116 | 17 |
Figure S19. Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D26V3.png)
P value = 5.38e-13 (Fisher's exact test), Q value = 4.8e-10
Table S20. Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
AMP PEAK 26(20Q12) CNV | 271 | 23 | 133 | 7 |
AMP PEAK 26(20Q12) WILD-TYPE | 85 | 31 | 10 | 6 |
Figure S20. Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D26V5.png)
P value = 4.17e-05 (Fisher's exact test), Q value = 0.036
Table S21. Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
AMP PEAK 26(20Q12) CNV | 74 | 137 | 135 | 73 |
AMP PEAK 26(20Q12) WILD-TYPE | 23 | 70 | 31 | 8 |
Figure S21. Get High-res Image Gene #26: 'Amp Peak 26(20q12)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D26V9.png)
P value = 2.18e-05 (Fisher's exact test), Q value = 0.019
Table S22. Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
AMP PEAK 27(20Q13.32) CNV | 299 | 141 |
AMP PEAK 27(20Q13.32) WILD-TYPE | 113 | 18 |
Figure S22. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D27V3.png)
P value = 8.76e-12 (Fisher's exact test), Q value = 7.8e-09
Table S23. Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
AMP PEAK 27(20Q13.32) CNV | 273 | 24 | 132 | 7 |
AMP PEAK 27(20Q13.32) WILD-TYPE | 83 | 30 | 11 | 6 |
Figure S23. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D27V5.png)
P value = 0.000131 (Fisher's exact test), Q value = 0.11
Table S24. Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
AMP PEAK 27(20Q13.32) CNV | 74 | 139 | 137 | 72 |
AMP PEAK 27(20Q13.32) WILD-TYPE | 23 | 68 | 29 | 9 |
Figure S24. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D27V9.png)
P value = 2.78e-05 (Fisher's exact test), Q value = 0.024
Table S25. Gene #38: 'Del Peak 10(4p16.1)' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'
nPatients | NO | YES |
---|---|---|
ALL | 9 | 566 |
DEL PEAK 10(4P16.1) CNV | 9 | 173 |
DEL PEAK 10(4P16.1) WILD-TYPE | 0 | 393 |
Figure S25. Get High-res Image Gene #38: 'Del Peak 10(4p16.1)' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'
![](D38V10.png)
P value = 2.4e-05 (Fisher's exact test), Q value = 0.021
Table S26. Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
DEL PEAK 18(8P23.2) CNV | 172 | 98 |
DEL PEAK 18(8P23.2) WILD-TYPE | 240 | 61 |
Figure S26. Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D46V3.png)
P value = 2.9e-05 (Fisher's exact test), Q value = 0.025
Table S27. Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
DEL PEAK 18(8P23.2) CNV | 156 | 15 | 89 | 7 |
DEL PEAK 18(8P23.2) WILD-TYPE | 200 | 39 | 54 | 6 |
Figure S27. Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D46V5.png)
P value = 2.78e-05 (Fisher's exact test), Q value = 0.024
Table S28. Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
DEL PEAK 18(8P23.2) CNV | 129 | 75 | 65 |
DEL PEAK 18(8P23.2) WILD-TYPE | 199 | 65 | 38 |
Figure S28. Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D46V7.png)
P value = 3.4e-05 (Fisher's exact test), Q value = 0.029
Table S29. Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
DEL PEAK 18(8P23.2) CNV | 39 | 78 | 92 | 52 |
DEL PEAK 18(8P23.2) WILD-TYPE | 58 | 129 | 74 | 29 |
Figure S29. Get High-res Image Gene #46: 'Del Peak 18(8p23.2)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D46V9.png)
P value = 0.000256 (Fisher's exact test), Q value = 0.22
Table S30. Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
DEL PEAK 19(8P22) CNV | 168 | 16 | 89 | 7 |
DEL PEAK 19(8P22) WILD-TYPE | 188 | 38 | 54 | 6 |
Figure S30. Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D47V5.png)
P value = 1.97e-06 (Fisher's exact test), Q value = 0.0017
Table S31. Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
DEL PEAK 19(8P22) CNV | 134 | 78 | 70 |
DEL PEAK 19(8P22) WILD-TYPE | 194 | 62 | 33 |
Figure S31. Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D47V7.png)
P value = 1.24e-06 (Fisher's exact test), Q value = 0.0011
Table S32. Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
DEL PEAK 19(8P22) CNV | 39 | 81 | 99 | 55 |
DEL PEAK 19(8P22) WILD-TYPE | 58 | 126 | 67 | 26 |
Figure S32. Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D47V9.png)
P value = 0.000106 (t-test), Q value = 0.091
Table S33. Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 538 | 2.2 (4.8) |
DEL PEAK 19(8P22) CNV | 271 | 3.0 (5.7) |
DEL PEAK 19(8P22) WILD-TYPE | 267 | 1.4 (3.3) |
Figure S33. Get High-res Image Gene #47: 'Del Peak 19(8p22)' versus Clinical Feature #12: 'NUMBER.OF.LYMPH.NODES'
![](D47V12.png)
P value = 1.15e-06 (Fisher's exact test), Q value = 0.001
Table S34. Gene #58: 'Del Peak 30(14q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
DEL PEAK 30(14Q22.1) CNV | 115 | 4 | 62 | 1 |
DEL PEAK 30(14Q22.1) WILD-TYPE | 241 | 50 | 81 | 12 |
Figure S34. Get High-res Image Gene #58: 'Del Peak 30(14q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D58V5.png)
P value = 4.34e-05 (logrank test), Q value = 0.037
Table S35. Gene #62: 'Del Peak 34(16p13.3)' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 444 | 60 | 0.1 - 135.5 (7.0) |
DEL PEAK 34(16P13.3) CNV | 42 | 13 | 0.2 - 49.9 (7.6) |
DEL PEAK 34(16P13.3) WILD-TYPE | 402 | 47 | 0.1 - 135.5 (7.0) |
Figure S35. Get High-res Image Gene #62: 'Del Peak 34(16p13.3)' versus Clinical Feature #1: 'Time to Death'
![](D62V1.png)
P value = 6.48e-08 (Fisher's exact test), Q value = 5.8e-05
Table S36. Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
DEL PEAK 36(17P12) CNV | 213 | 14 | 103 | 6 |
DEL PEAK 36(17P12) WILD-TYPE | 143 | 40 | 40 | 7 |
Figure S36. Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D64V5.png)
P value = 0.000121 (Fisher's exact test), Q value = 0.1
Table S37. Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
DEL PEAK 36(17P12) CNV | 171 | 95 | 74 |
DEL PEAK 36(17P12) WILD-TYPE | 157 | 45 | 29 |
Figure S37. Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D64V7.png)
P value = 3.15e-05 (Fisher's exact test), Q value = 0.027
Table S38. Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
DEL PEAK 36(17P12) CNV | 50 | 104 | 116 | 59 |
DEL PEAK 36(17P12) WILD-TYPE | 47 | 103 | 50 | 22 |
Figure S38. Get High-res Image Gene #64: 'Del Peak 36(17p12)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D64V9.png)
P value = 1.82e-06 (Fisher's exact test), Q value = 0.0016
Table S39. Gene #66: 'Del Peak 38(18p11.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
DEL PEAK 38(18P11.31) CNV | 219 | 119 |
DEL PEAK 38(18P11.31) WILD-TYPE | 193 | 40 |
Figure S39. Get High-res Image Gene #66: 'Del Peak 38(18p11.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D66V3.png)
P value = 1.53e-16 (Fisher's exact test), Q value = 1.4e-13
Table S40. Gene #66: 'Del Peak 38(18p11.31)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
DEL PEAK 38(18P11.31) CNV | 211 | 7 | 113 | 6 |
DEL PEAK 38(18P11.31) WILD-TYPE | 145 | 47 | 30 | 7 |
Figure S40. Get High-res Image Gene #66: 'Del Peak 38(18p11.31)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D66V5.png)
P value = 1.57e-09 (Fisher's exact test), Q value = 1.4e-06
Table S41. Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
DEL PEAK 39(18Q12.2) CNV | 247 | 136 |
DEL PEAK 39(18Q12.2) WILD-TYPE | 165 | 23 |
Figure S41. Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D67V3.png)
P value = 8.59e-18 (Fisher's exact test), Q value = 7.7e-15
Table S42. Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
DEL PEAK 39(18Q12.2) CNV | 235 | 11 | 125 | 10 |
DEL PEAK 39(18Q12.2) WILD-TYPE | 121 | 43 | 18 | 3 |
Figure S42. Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D67V5.png)
P value = 0.000131 (Fisher's exact test), Q value = 0.11
Table S43. Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
DEL PEAK 39(18Q12.2) CNV | 196 | 107 | 79 |
DEL PEAK 39(18Q12.2) WILD-TYPE | 132 | 33 | 24 |
Figure S43. Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D67V7.png)
P value = 6.82e-05 (Fisher's exact test), Q value = 0.059
Table S44. Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
DEL PEAK 39(18Q12.2) CNV | 56 | 122 | 121 | 67 |
DEL PEAK 39(18Q12.2) WILD-TYPE | 41 | 85 | 45 | 14 |
Figure S44. Get High-res Image Gene #67: 'Del Peak 39(18q12.2)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D67V9.png)
P value = 1.07e-09 (Fisher's exact test), Q value = 9.6e-07
Table S45. Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
DEL PEAK 40(18Q21.2) CNV | 260 | 140 |
DEL PEAK 40(18Q21.2) WILD-TYPE | 152 | 19 |
Figure S45. Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D68V3.png)
P value = 3.7e-16 (Fisher's exact test), Q value = 3.3e-13
Table S46. Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
DEL PEAK 40(18Q21.2) CNV | 245 | 14 | 126 | 12 |
DEL PEAK 40(18Q21.2) WILD-TYPE | 111 | 40 | 17 | 1 |
Figure S46. Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D68V5.png)
P value = 1.95e-06 (Fisher's exact test), Q value = 0.0017
Table S47. Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
DEL PEAK 40(18Q21.2) CNV | 202 | 111 | 86 |
DEL PEAK 40(18Q21.2) WILD-TYPE | 126 | 29 | 17 |
Figure S47. Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D68V7.png)
P value = 4.1e-07 (Fisher's exact test), Q value = 0.00036
Table S48. Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
DEL PEAK 40(18Q21.2) CNV | 58 | 126 | 128 | 72 |
DEL PEAK 40(18Q21.2) WILD-TYPE | 39 | 81 | 38 | 9 |
Figure S48. Get High-res Image Gene #68: 'Del Peak 40(18q21.2)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D68V9.png)
P value = 1.94e-07 (Fisher's exact test), Q value = 0.00017
Table S49. Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 159 |
DEL PEAK 41(18Q22.1) CNV | 260 | 135 |
DEL PEAK 41(18Q22.1) WILD-TYPE | 152 | 24 |
Figure S49. Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'
![](D69V3.png)
P value = 2.07e-15 (Fisher's exact test), Q value = 1.9e-12
Table S50. Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 143 | 13 |
DEL PEAK 41(18Q22.1) CNV | 246 | 13 | 124 | 10 |
DEL PEAK 41(18Q22.1) WILD-TYPE | 110 | 41 | 19 | 3 |
Figure S50. Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'
![](D69V5.png)
P value = 1.14e-05 (Fisher's exact test), Q value = 0.01
Table S51. Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
DEL PEAK 41(18Q22.1) CNV | 201 | 108 | 85 |
DEL PEAK 41(18Q22.1) WILD-TYPE | 127 | 32 | 18 |
Figure S51. Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D69V7.png)
P value = 4.68e-06 (Fisher's exact test), Q value = 0.0041
Table S52. Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #9: 'TUMOR.STAGE'
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 97 | 207 | 166 | 81 |
DEL PEAK 41(18Q22.1) CNV | 58 | 126 | 124 | 71 |
DEL PEAK 41(18Q22.1) WILD-TYPE | 39 | 81 | 42 | 10 |
Figure S52. Get High-res Image Gene #69: 'Del Peak 41(18q22.1)' versus Clinical Feature #9: 'TUMOR.STAGE'
![](D69V9.png)
P value = 7.64e-05 (Fisher's exact test), Q value = 0.066
Table S53. Gene #70: 'Del Peak 42(19p13.3)' versus Clinical Feature #7: 'PATHOLOGY.N'
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 328 | 140 | 103 |
DEL PEAK 42(19P13.3) CNV | 36 | 26 | 30 |
DEL PEAK 42(19P13.3) WILD-TYPE | 292 | 114 | 73 |
Figure S53. Get High-res Image Gene #70: 'Del Peak 42(19p13.3)' versus Clinical Feature #7: 'PATHOLOGY.N'
![](D70V7.png)
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = COADREAD-TP.clin.merged.picked.txt
-
Number of patients = 575
-
Number of significantly arm-level cnvs = 75
-
Number of selected clinical features = 12
-
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.