This pipeline computes the correlation between significant copy number variation (cnv) genes and selected clinical features.
Testing the association between copy number variation of 78 peak regions and 10 clinical features across 574 patients, 34 significant findings detected with Q value < 0.25.
-
Amp Peak 5(6p21.1) cnvs correlated to 'PATHOLOGY.N'.
-
Amp Peak 6(7p11.2) cnvs correlated to 'HISTOLOGICAL.TYPE'.
-
Amp Peak 11(9p13.3) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE'.
-
Amp Peak 15(13q12.13) cnvs correlated to 'HISTOLOGICAL.TYPE'.
-
Amp Peak 16(13q12.2) cnvs correlated to 'HISTOLOGICAL.TYPE'.
-
Amp Peak 17(13q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'PATHOLOGY.N'.
-
Amp Peak 26(20p11.23) cnvs correlated to 'HISTOLOGICAL.TYPE'.
-
Amp Peak 27(20p11.21) cnvs correlated to 'HISTOLOGICAL.TYPE'.
-
Amp Peak 28(20q11.21) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
-
Amp Peak 29(20q13.12) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
-
Amp Peak 30(20q13.32) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
-
Del Peak 2(1p36.11) cnvs correlated to 'HISTOLOGICAL.TYPE'.
-
Del Peak 14(4q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE'.
-
Del Peak 22(8p23.2) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'PATHOLOGY.N'.
-
Del Peak 23(8p22) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'PATHOLOGY.N'.
-
Del Peak 32(14q11.2) cnvs correlated to 'HISTOLOGICAL.TYPE'.
-
Del Peak 35(15q22.33) cnvs correlated to 'HISTOLOGICAL.TYPE'.
-
Del Peak 38(17p12) cnvs correlated to 'HISTOLOGICAL.TYPE'.
-
Del Peak 40(18p11.31) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
-
Del Peak 41(18q12.2) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
-
Del Peak 42(18q21.2) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.N'.
-
Del Peak 43(18q22.1) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.N'.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
GENDER |
HISTOLOGICAL TYPE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
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 | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | |
Del Peak 42(18q21 2) | 374 (65%) | 200 |
0.295 (1.00) |
0.22 (1.00) |
4.62e-07 (0.000355) |
0.254 (1.00) |
6.42e-12 (4.97e-09) |
0.158 (1.00) |
4.08e-06 (0.00312) |
0.000966 (0.708) |
0.507 (1.00) |
0.802 (1.00) |
Del Peak 43(18q22 1) | 369 (64%) | 205 |
0.19 (1.00) |
0.487 (1.00) |
9.83e-06 (0.00751) |
0.433 (1.00) |
1.25e-12 (9.72e-10) |
0.203 (1.00) |
2.06e-05 (0.0157) |
0.00323 (1.00) |
0.501 (1.00) |
1 (1.00) |
Amp Peak 17(13q22 1) | 336 (59%) | 238 |
0.255 (1.00) |
0.756 (1.00) |
0.00803 (1.00) |
0.174 (1.00) |
1.05e-07 (8.1e-05) |
0.745 (1.00) |
0.000212 (0.159) |
0.116 (1.00) |
0.318 (1.00) |
0.545 (1.00) |
Amp Peak 28(20q11 21) | 403 (70%) | 171 |
0.84 (1.00) |
0.683 (1.00) |
2.57e-05 (0.0195) |
0.36 (1.00) |
2.31e-15 (1.8e-12) |
0.262 (1.00) |
0.0217 (1.00) |
0.135 (1.00) |
0.73 (1.00) |
0.516 (1.00) |
Amp Peak 29(20q13 12) | 412 (72%) | 162 |
0.424 (1.00) |
0.972 (1.00) |
7.52e-05 (0.0569) |
0.516 (1.00) |
1.44e-13 (1.12e-10) |
0.465 (1.00) |
0.00756 (1.00) |
0.0333 (1.00) |
0.717 (1.00) |
0.508 (1.00) |
Amp Peak 30(20q13 32) | 414 (72%) | 160 |
0.409 (1.00) |
0.701 (1.00) |
0.000157 (0.118) |
0.642 (1.00) |
1.34e-13 (1.04e-10) |
0.469 (1.00) |
0.00522 (1.00) |
0.0254 (1.00) |
0.714 (1.00) |
0.595 (1.00) |
Del Peak 22(8p23 2) | 244 (43%) | 330 |
0.397 (1.00) |
0.656 (1.00) |
0.000444 (0.329) |
0.31 (1.00) |
8.34e-05 (0.063) |
0.207 (1.00) |
0.000169 (0.127) |
0.0413 (1.00) |
0.505 (1.00) |
0.336 (1.00) |
Del Peak 23(8p22) | 256 (45%) | 318 |
0.246 (1.00) |
0.717 (1.00) |
0.000996 (0.727) |
0.614 (1.00) |
1.88e-05 (0.0143) |
0.106 (1.00) |
2.41e-05 (0.0183) |
0.043 (1.00) |
0.521 (1.00) |
0.472 (1.00) |
Del Peak 40(18p11 31) | 312 (54%) | 262 |
0.822 (1.00) |
0.319 (1.00) |
1.41e-05 (0.0107) |
0.675 (1.00) |
9.2e-15 (7.17e-12) |
0.685 (1.00) |
0.00512 (1.00) |
0.00948 (1.00) |
0.738 (1.00) |
1 (1.00) |
Del Peak 41(18q12 2) | 356 (62%) | 218 |
0.86 (1.00) |
0.303 (1.00) |
8.03e-07 (0.000616) |
0.547 (1.00) |
5.73e-14 (4.46e-11) |
0.215 (1.00) |
0.000453 (0.335) |
0.025 (1.00) |
0.494 (1.00) |
0.807 (1.00) |
Amp Peak 5(6p21 1) | 102 (18%) | 472 |
0.349 (1.00) |
0.535 (1.00) |
0.00681 (1.00) |
0.512 (1.00) |
0.00171 (1.00) |
0.318 (1.00) |
0.000301 (0.225) |
0.124 (1.00) |
0.204 (1.00) |
0.755 (1.00) |
Amp Peak 6(7p11 2) | 282 (49%) | 292 |
0.118 (1.00) |
0.709 (1.00) |
0.261 (1.00) |
0.558 (1.00) |
0.000102 (0.077) |
0.796 (1.00) |
0.00877 (1.00) |
0.0479 (1.00) |
0.748 (1.00) |
0.905 (1.00) |
Amp Peak 11(9p13 3) | 87 (15%) | 487 |
0.407 (1.00) |
0.565 (1.00) |
7.82e-05 (0.0591) |
1 (1.00) |
0.000405 (0.301) |
0.793 (1.00) |
0.684 (1.00) |
0.777 (1.00) |
1 (1.00) |
0.319 (1.00) |
Amp Peak 15(13q12 13) | 339 (59%) | 235 |
0.589 (1.00) |
0.636 (1.00) |
0.00121 (0.877) |
0.932 (1.00) |
5.34e-10 (4.13e-07) |
0.692 (1.00) |
0.000574 (0.423) |
0.036 (1.00) |
0.744 (1.00) |
0.547 (1.00) |
Amp Peak 16(13q12 2) | 333 (58%) | 241 |
0.516 (1.00) |
0.499 (1.00) |
0.00173 (1.00) |
0.799 (1.00) |
2.15e-09 (1.66e-06) |
0.622 (1.00) |
0.000796 (0.584) |
0.0607 (1.00) |
0.741 (1.00) |
0.629 (1.00) |
Amp Peak 26(20p11 23) | 257 (45%) | 317 |
0.932 (1.00) |
0.32 (1.00) |
0.00487 (1.00) |
0.078 (1.00) |
1.09e-06 (0.000835) |
0.709 (1.00) |
0.0774 (1.00) |
0.0715 (1.00) |
0.523 (1.00) |
0.15 (1.00) |
Amp Peak 27(20p11 21) | 294 (51%) | 280 |
0.82 (1.00) |
0.67 (1.00) |
0.00888 (1.00) |
0.0789 (1.00) |
1.71e-08 (1.32e-05) |
0.309 (1.00) |
0.823 (1.00) |
0.102 (1.00) |
1 (1.00) |
0.721 (1.00) |
Del Peak 2(1p36 11) | 166 (29%) | 408 |
0.0371 (1.00) |
0.351 (1.00) |
0.351 (1.00) |
0.58 (1.00) |
0.000257 (0.193) |
0.283 (1.00) |
0.00848 (1.00) |
0.0013 (0.942) |
1 (1.00) |
0.149 (1.00) |
Del Peak 14(4q22 1) | 140 (24%) | 434 |
0.196 (1.00) |
0.959 (1.00) |
0.0043 (1.00) |
0.244 (1.00) |
0.000137 (0.103) |
0.472 (1.00) |
0.0327 (1.00) |
0.343 (1.00) |
0.043 (1.00) |
0.211 (1.00) |
Del Peak 32(14q11 2) | 149 (26%) | 425 |
0.151 (1.00) |
0.465 (1.00) |
0.0181 (1.00) |
0.775 (1.00) |
1.45e-05 (0.011) |
0.642 (1.00) |
0.0342 (1.00) |
0.556 (1.00) |
0.702 (1.00) |
0.892 (1.00) |
Del Peak 35(15q22 33) | 160 (28%) | 414 |
0.343 (1.00) |
0.912 (1.00) |
0.000775 (0.57) |
0.78 (1.00) |
0.000171 (0.128) |
0.0449 (1.00) |
0.0684 (1.00) |
0.32 (1.00) |
0.273 (1.00) |
0.791 (1.00) |
Del Peak 38(17p12) | 300 (52%) | 274 |
0.524 (1.00) |
0.301 (1.00) |
0.00367 (1.00) |
0.452 (1.00) |
1.84e-07 (0.000142) |
0.699 (1.00) |
0.00777 (1.00) |
0.0611 (1.00) |
0.18 (1.00) |
0.72 (1.00) |
Amp Peak 1(1q21 3) | 100 (17%) | 474 |
0.897 (1.00) |
0.682 (1.00) |
0.107 (1.00) |
0.0618 (1.00) |
0.195 (1.00) |
0.317 (1.00) |
0.229 (1.00) |
0.377 (1.00) |
0.66 (1.00) |
0.875 (1.00) |
Amp Peak 2(2q33 1) | 76 (13%) | 498 |
0.933 (1.00) |
0.636 (1.00) |
0.129 (1.00) |
0.109 (1.00) |
0.0143 (1.00) |
0.909 (1.00) |
0.0404 (1.00) |
0.933 (1.00) |
1 (1.00) |
0.29 (1.00) |
Amp Peak 3(4q28 3) | 19 (3%) | 555 |
0.341 (1.00) |
0.35 (1.00) |
0.191 (1.00) |
0.243 (1.00) |
0.238 (1.00) |
0.217 (1.00) |
0.768 (1.00) |
0.0962 (1.00) |
0.263 (1.00) |
1 (1.00) |
Amp Peak 4(5p13 2) | 84 (15%) | 490 |
0.181 (1.00) |
0.91 (1.00) |
0.356 (1.00) |
0.906 (1.00) |
0.234 (1.00) |
0.401 (1.00) |
0.532 (1.00) |
0.948 (1.00) |
0.626 (1.00) |
0.613 (1.00) |
Amp Peak 7(8p11 23) | 155 (27%) | 419 |
0.37 (1.00) |
0.993 (1.00) |
0.916 (1.00) |
0.347 (1.00) |
0.524 (1.00) |
0.359 (1.00) |
0.672 (1.00) |
0.616 (1.00) |
0.708 (1.00) |
0.687 (1.00) |
Amp Peak 8(8p11 21) | 195 (34%) | 379 |
0.781 (1.00) |
0.624 (1.00) |
0.375 (1.00) |
0.134 (1.00) |
0.264 (1.00) |
0.376 (1.00) |
0.493 (1.00) |
0.501 (1.00) |
0.725 (1.00) |
0.9 (1.00) |
Amp Peak 9(8q11 23) | 239 (42%) | 335 |
0.702 (1.00) |
0.235 (1.00) |
0.0717 (1.00) |
0.498 (1.00) |
0.0171 (1.00) |
0.386 (1.00) |
0.0999 (1.00) |
0.209 (1.00) |
0.742 (1.00) |
0.717 (1.00) |
Amp Peak 10(8q24 21) | 293 (51%) | 281 |
0.467 (1.00) |
0.128 (1.00) |
0.0754 (1.00) |
0.503 (1.00) |
0.0302 (1.00) |
0.455 (1.00) |
0.0267 (1.00) |
0.0262 (1.00) |
0.747 (1.00) |
0.635 (1.00) |
Amp Peak 12(10q23 1) | 25 (4%) | 549 |
0.603 (1.00) |
0.0542 (1.00) |
0.363 (1.00) |
0.683 (1.00) |
0.502 (1.00) |
0.0806 (1.00) |
0.0148 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.77 (1.00) |
Amp Peak 13(11p15 5) | 102 (18%) | 472 |
0.814 (1.00) |
0.217 (1.00) |
0.00977 (1.00) |
0.446 (1.00) |
0.000538 (0.397) |
0.218 (1.00) |
0.186 (1.00) |
0.125 (1.00) |
0.665 (1.00) |
0.532 (1.00) |
Amp Peak 14(12p13 32) | 115 (20%) | 459 |
0.599 (1.00) |
0.00701 (1.00) |
0.907 (1.00) |
1 (1.00) |
0.59 (1.00) |
0.746 (1.00) |
0.00879 (1.00) |
0.27 (1.00) |
1 (1.00) |
0.372 (1.00) |
Amp Peak 18(15q26 1) | 25 (4%) | 549 |
0.187 (1.00) |
0.732 (1.00) |
1 (1.00) |
0.683 (1.00) |
0.794 (1.00) |
0.979 (1.00) |
0.0312 (1.00) |
0.414 (1.00) |
1 (1.00) |
0.77 (1.00) |
Amp Peak 19(16p11 2) | 123 (21%) | 451 |
0.988 (1.00) |
0.748 (1.00) |
0.82 (1.00) |
0.476 (1.00) |
0.005 (1.00) |
0.758 (1.00) |
0.000427 (0.317) |
0.337 (1.00) |
0.412 (1.00) |
0.145 (1.00) |
Amp Peak 20(16q12 1) | 108 (19%) | 466 |
0.779 (1.00) |
0.238 (1.00) |
0.472 (1.00) |
0.593 (1.00) |
0.00561 (1.00) |
0.66 (1.00) |
0.000664 (0.488) |
0.449 (1.00) |
0.381 (1.00) |
0.0315 (1.00) |
Amp Peak 21(17q12) | 99 (17%) | 475 |
0.271 (1.00) |
0.391 (1.00) |
0.538 (1.00) |
0.0271 (1.00) |
0.0151 (1.00) |
0.6 (1.00) |
0.286 (1.00) |
0.0438 (1.00) |
1 (1.00) |
0.0175 (1.00) |
Amp Peak 22(17q24 1) | 92 (16%) | 482 |
0.0245 (1.00) |
0.197 (1.00) |
0.702 (1.00) |
0.733 (1.00) |
0.0846 (1.00) |
0.687 (1.00) |
0.723 (1.00) |
0.121 (1.00) |
1 (1.00) |
0.00845 (1.00) |
Amp Peak 23(19q12) | 82 (14%) | 492 |
0.911 (1.00) |
0.75 (1.00) |
0.109 (1.00) |
0.634 (1.00) |
0.0209 (1.00) |
0.937 (1.00) |
0.222 (1.00) |
0.642 (1.00) |
0.371 (1.00) |
0.495 (1.00) |
Amp Peak 24(19q13 12) | 78 (14%) | 496 |
0.135 (1.00) |
0.974 (1.00) |
0.173 (1.00) |
0.903 (1.00) |
0.115 (1.00) |
0.911 (1.00) |
0.58 (1.00) |
0.855 (1.00) |
0.617 (1.00) |
0.301 (1.00) |
Amp Peak 25(20p12 1) | 213 (37%) | 361 |
0.764 (1.00) |
0.179 (1.00) |
0.148 (1.00) |
0.00947 (1.00) |
0.000393 (0.292) |
0.305 (1.00) |
0.33 (1.00) |
0.0304 (1.00) |
0.303 (1.00) |
1 (1.00) |
Del Peak 1(1p36 21) | 151 (26%) | 423 |
0.106 (1.00) |
0.591 (1.00) |
0.0423 (1.00) |
0.343 (1.00) |
0.00385 (1.00) |
0.868 (1.00) |
0.0264 (1.00) |
0.00933 (1.00) |
1 (1.00) |
0.139 (1.00) |
Del Peak 3(1p33) | 103 (18%) | 471 |
0.00682 (1.00) |
0.561 (1.00) |
0.542 (1.00) |
0.664 (1.00) |
0.251 (1.00) |
0.173 (1.00) |
0.0469 (1.00) |
0.0187 (1.00) |
1 (1.00) |
0.163 (1.00) |
Del Peak 4(1p13 2) | 103 (18%) | 471 |
0.11 (1.00) |
0.567 (1.00) |
0.714 (1.00) |
0.586 (1.00) |
0.172 (1.00) |
0.141 (1.00) |
0.153 (1.00) |
0.00224 (1.00) |
0.667 (1.00) |
0.0871 (1.00) |
Del Peak 5(1q42 3) | 28 (5%) | 546 |
0.96 (1.00) |
0.75 (1.00) |
0.832 (1.00) |
1 (1.00) |
1 (1.00) |
0.505 (1.00) |
0.146 (1.00) |
0.867 (1.00) |
1 (1.00) |
0.406 (1.00) |
Del Peak 6(2p21) | 21 (4%) | 553 |
0.767 (1.00) |
0.83 (1.00) |
0.0219 (1.00) |
0.183 (1.00) |
0.0649 (1.00) |
0.739 (1.00) |
0.393 (1.00) |
0.794 (1.00) |
0.287 (1.00) |
0.754 (1.00) |
Del Peak 7(2p12) | 23 (4%) | 551 |
0.822 (1.00) |
0.499 (1.00) |
0.00117 (0.856) |
0.833 (1.00) |
0.00976 (1.00) |
0.265 (1.00) |
0.538 (1.00) |
0.789 (1.00) |
0.31 (1.00) |
1 (1.00) |
Del Peak 8(2q22 1) | 20 (3%) | 554 |
0.754 (1.00) |
0.987 (1.00) |
1 (1.00) |
0.364 (1.00) |
0.487 (1.00) |
0.481 (1.00) |
0.704 (1.00) |
0.184 (1.00) |
1 (1.00) |
0.754 (1.00) |
Del Peak 9(2q37 2) | 21 (4%) | 553 |
0.55 (1.00) |
0.504 (1.00) |
0.807 (1.00) |
0.659 (1.00) |
0.927 (1.00) |
0.329 (1.00) |
0.46 (1.00) |
0.368 (1.00) |
1 (1.00) |
0.0572 (1.00) |
Del Peak 10(3p26 3) | 58 (10%) | 516 |
0.000381 (0.284) |
0.306 (1.00) |
0.643 (1.00) |
0.331 (1.00) |
0.0449 (1.00) |
0.0245 (1.00) |
0.0184 (1.00) |
0.000487 (0.36) |
1 (1.00) |
1 (1.00) |
Del Peak 11(3p14 2) | 80 (14%) | 494 |
0.276 (1.00) |
0.749 (1.00) |
1 (1.00) |
0.63 (1.00) |
0.507 (1.00) |
0.182 (1.00) |
0.292 (1.00) |
0.0125 (1.00) |
1 (1.00) |
0.302 (1.00) |
Del Peak 12(3q26 31) | 35 (6%) | 539 |
0.641 (1.00) |
0.843 (1.00) |
0.435 (1.00) |
0.035 (1.00) |
0.0209 (1.00) |
0.357 (1.00) |
0.516 (1.00) |
0.233 (1.00) |
1 (1.00) |
0.209 (1.00) |
Del Peak 13(4p16 2) | 131 (23%) | 443 |
0.00429 (1.00) |
0.379 (1.00) |
0.094 (1.00) |
0.135 (1.00) |
0.0225 (1.00) |
0.901 (1.00) |
0.00517 (1.00) |
0.0173 (1.00) |
0.00581 (1.00) |
0.0323 (1.00) |
Del Peak 15(4q35 1) | 151 (26%) | 423 |
0.695 (1.00) |
0.579 (1.00) |
0.134 (1.00) |
0.85 (1.00) |
0.00241 (1.00) |
0.864 (1.00) |
0.0876 (1.00) |
0.856 (1.00) |
0.0124 (1.00) |
0.416 (1.00) |
Del Peak 16(5q11 2) | 95 (17%) | 479 |
0.791 (1.00) |
0.74 (1.00) |
0.0173 (1.00) |
0.261 (1.00) |
0.0173 (1.00) |
0.976 (1.00) |
0.0725 (1.00) |
0.223 (1.00) |
0.00098 (0.716) |
0.425 (1.00) |
Del Peak 17(5q21 1) | 112 (20%) | 462 |
0.571 (1.00) |
0.943 (1.00) |
0.815 (1.00) |
0.141 (1.00) |
0.615 (1.00) |
0.919 (1.00) |
0.127 (1.00) |
0.223 (1.00) |
0.0168 (1.00) |
0.549 (1.00) |
Del Peak 18(5q22 2) | 124 (22%) | 450 |
0.53 (1.00) |
0.632 (1.00) |
0.308 (1.00) |
0.0843 (1.00) |
0.161 (1.00) |
0.934 (1.00) |
0.416 (1.00) |
0.831 (1.00) |
0.00431 (1.00) |
0.472 (1.00) |
Del Peak 19(6p25 3) | 47 (8%) | 527 |
0.862 (1.00) |
0.164 (1.00) |
0.227 (1.00) |
0.169 (1.00) |
0.147 (1.00) |
0.138 (1.00) |
0.709 (1.00) |
0.614 (1.00) |
0.539 (1.00) |
0.284 (1.00) |
Del Peak 20(6q26) | 48 (8%) | 526 |
0.00253 (1.00) |
0.675 (1.00) |
0.302 (1.00) |
0.547 (1.00) |
0.0618 (1.00) |
0.14 (1.00) |
0.00236 (1.00) |
0.00123 (0.89) |
0.547 (1.00) |
0.523 (1.00) |
Del Peak 21(7q31 1) | 12 (2%) | 562 |
0.891 (1.00) |
0.313 (1.00) |
0.745 (1.00) |
0.561 (1.00) |
0.417 (1.00) |
0.681 (1.00) |
0.0907 (1.00) |
0.452 (1.00) |
1 (1.00) |
1 (1.00) |
Del Peak 24(8p11 21) | 96 (17%) | 478 |
0.0894 (1.00) |
0.771 (1.00) |
0.259 (1.00) |
0.37 (1.00) |
0.254 (1.00) |
0.914 (1.00) |
0.0198 (1.00) |
0.479 (1.00) |
1 (1.00) |
0.749 (1.00) |
Del Peak 25(8p11 21) | 49 (9%) | 525 |
0.14 (1.00) |
0.219 (1.00) |
0.866 (1.00) |
0.881 (1.00) |
0.641 (1.00) |
0.677 (1.00) |
0.0413 (1.00) |
0.0728 (1.00) |
0.555 (1.00) |
0.523 (1.00) |
Del Peak 26(10q21 1) | 68 (12%) | 506 |
0.449 (1.00) |
0.159 (1.00) |
0.0214 (1.00) |
0.898 (1.00) |
0.0251 (1.00) |
0.815 (1.00) |
0.418 (1.00) |
0.53 (1.00) |
1 (1.00) |
0.712 (1.00) |
Del Peak 27(10q23 31) | 86 (15%) | 488 |
0.331 (1.00) |
0.0655 (1.00) |
0.00571 (1.00) |
0.641 (1.00) |
0.0144 (1.00) |
0.219 (1.00) |
0.149 (1.00) |
0.0227 (1.00) |
0.63 (1.00) |
0.403 (1.00) |
Del Peak 28(10q25 2) | 81 (14%) | 493 |
0.722 (1.00) |
0.164 (1.00) |
0.0153 (1.00) |
0.631 (1.00) |
0.0257 (1.00) |
0.301 (1.00) |
0.1 (1.00) |
0.363 (1.00) |
0.37 (1.00) |
0.732 (1.00) |
Del Peak 29(11q22 3) | 72 (13%) | 502 |
0.905 (1.00) |
0.85 (1.00) |
0.00157 (1.00) |
0.531 (1.00) |
0.000973 (0.712) |
0.522 (1.00) |
0.312 (1.00) |
0.968 (1.00) |
0.0911 (1.00) |
1 (1.00) |
Del Peak 30(12p13 1) | 47 (8%) | 527 |
0.0244 (1.00) |
0.669 (1.00) |
0.0141 (1.00) |
0.224 (1.00) |
0.00338 (1.00) |
0.31 (1.00) |
0.0243 (1.00) |
0.185 (1.00) |
0.163 (1.00) |
0.284 (1.00) |
Del Peak 31(12q21 2) | 40 (7%) | 534 |
0.841 (1.00) |
0.889 (1.00) |
0.278 (1.00) |
0.324 (1.00) |
0.0609 (1.00) |
0.497 (1.00) |
0.0894 (1.00) |
0.0012 (0.873) |
0.48 (1.00) |
1 (1.00) |
Del Peak 33(15q11 2) | 178 (31%) | 396 |
0.986 (1.00) |
0.481 (1.00) |
0.0676 (1.00) |
0.857 (1.00) |
0.00259 (1.00) |
0.468 (1.00) |
0.0486 (1.00) |
0.334 (1.00) |
0.469 (1.00) |
0.52 (1.00) |
Del Peak 34(15q21 1) | 174 (30%) | 400 |
0.36 (1.00) |
0.973 (1.00) |
0.00799 (1.00) |
0.785 (1.00) |
0.0025 (1.00) |
0.513 (1.00) |
0.126 (1.00) |
0.245 (1.00) |
0.465 (1.00) |
0.604 (1.00) |
Del Peak 36(16p13 3) | 43 (7%) | 531 |
0.00619 (1.00) |
0.546 (1.00) |
0.597 (1.00) |
0.874 (1.00) |
0.296 (1.00) |
0.119 (1.00) |
0.388 (1.00) |
0.562 (1.00) |
1 (1.00) |
0.821 (1.00) |
Del Peak 37(16q23 1) | 54 (9%) | 520 |
0.0199 (1.00) |
0.075 (1.00) |
0.34 (1.00) |
0.197 (1.00) |
0.379 (1.00) |
0.527 (1.00) |
0.618 (1.00) |
0.857 (1.00) |
0.592 (1.00) |
1 (1.00) |
Del Peak 39(17q24 3) | 59 (10%) | 515 |
0.278 (1.00) |
0.356 (1.00) |
0.283 (1.00) |
0.409 (1.00) |
0.619 (1.00) |
0.392 (1.00) |
0.0188 (1.00) |
0.121 (1.00) |
0.234 (1.00) |
0.113 (1.00) |
Del Peak 44(19p13 3) | 50 (9%) | 524 |
0.465 (1.00) |
0.74 (1.00) |
0.322 (1.00) |
0.138 (1.00) |
0.0487 (1.00) |
0.94 (1.00) |
0.108 (1.00) |
0.54 (1.00) |
1 (1.00) |
0.832 (1.00) |
Del Peak 45(20p12 1) | 107 (19%) | 467 |
0.921 (1.00) |
0.599 (1.00) |
0.0157 (1.00) |
0.668 (1.00) |
0.0127 (1.00) |
0.809 (1.00) |
0.527 (1.00) |
0.376 (1.00) |
0.221 (1.00) |
0.646 (1.00) |
Del Peak 46(21q11 2) | 137 (24%) | 437 |
0.973 (1.00) |
0.741 (1.00) |
0.0203 (1.00) |
1 (1.00) |
0.00287 (1.00) |
0.657 (1.00) |
0.273 (1.00) |
0.496 (1.00) |
0.452 (1.00) |
0.576 (1.00) |
Del Peak 47(21q22 2) | 123 (21%) | 451 |
0.29 (1.00) |
0.668 (1.00) |
0.00195 (1.00) |
0.262 (1.00) |
0.00138 (1.00) |
0.402 (1.00) |
0.278 (1.00) |
0.75 (1.00) |
1 (1.00) |
0.771 (1.00) |
Del Peak 48(22q13 31) | 141 (25%) | 433 |
0.333 (1.00) |
0.0663 (1.00) |
0.0163 (1.00) |
0.498 (1.00) |
0.000375 (0.28) |
0.505 (1.00) |
0.00211 (1.00) |
0.0457 (1.00) |
0.234 (1.00) |
0.168 (1.00) |
P value = 0.000301 (Fisher's exact test), Q value = 0.22
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 327 | 140 | 103 |
AMP PEAK 5(6P21.1) MUTATED | 43 | 26 | 32 |
AMP PEAK 5(6P21.1) WILD-TYPE | 284 | 114 | 71 |
P value = 0.000102 (Fisher's exact test), Q value = 0.077
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
AMP PEAK 6(7P11.2) MUTATED | 181 | 15 | 82 | 2 |
AMP PEAK 6(7P11.2) WILD-TYPE | 175 | 39 | 60 | 11 |
P value = 7.82e-05 (Fisher's exact test), Q value = 0.059
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 158 |
AMP PEAK 11(9P13.3) MUTATED | 47 | 40 |
AMP PEAK 11(9P13.3) WILD-TYPE | 365 | 118 |
P value = 5.34e-10 (Fisher's exact test), Q value = 4.1e-07
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
AMP PEAK 15(13Q12.13) MUTATED | 212 | 13 | 105 | 4 |
AMP PEAK 15(13Q12.13) WILD-TYPE | 144 | 41 | 37 | 9 |
P value = 2.15e-09 (Fisher's exact test), Q value = 1.7e-06
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
AMP PEAK 16(13Q12.2) MUTATED | 208 | 13 | 103 | 4 |
AMP PEAK 16(13Q12.2) WILD-TYPE | 148 | 41 | 39 | 9 |
P value = 1.05e-07 (Fisher's exact test), Q value = 8.1e-05
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
AMP PEAK 17(13Q22.1) MUTATED | 211 | 15 | 101 | 4 |
AMP PEAK 17(13Q22.1) WILD-TYPE | 145 | 39 | 41 | 9 |
P value = 0.000212 (Fisher's exact test), Q value = 0.16
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 327 | 140 | 103 |
AMP PEAK 17(13Q22.1) MUTATED | 167 | 98 | 67 |
AMP PEAK 17(13Q22.1) WILD-TYPE | 160 | 42 | 36 |
P value = 1.09e-06 (Fisher's exact test), Q value = 0.00083
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
AMP PEAK 26(20P11.23) MUTATED | 159 | 9 | 81 | 3 |
AMP PEAK 26(20P11.23) WILD-TYPE | 197 | 45 | 61 | 10 |
P value = 1.71e-08 (Fisher's exact test), Q value = 1.3e-05
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
AMP PEAK 27(20P11.21) MUTATED | 185 | 10 | 91 | 3 |
AMP PEAK 27(20P11.21) WILD-TYPE | 171 | 44 | 51 | 10 |
P value = 2.57e-05 (Fisher's exact test), Q value = 0.019
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 158 |
AMP PEAK 28(20Q11.21) MUTATED | 269 | 131 |
AMP PEAK 28(20Q11.21) WILD-TYPE | 143 | 27 |
P value = 2.31e-15 (Fisher's exact test), Q value = 1.8e-12
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
AMP PEAK 28(20Q11.21) MUTATED | 253 | 14 | 123 | 6 |
AMP PEAK 28(20Q11.21) WILD-TYPE | 103 | 40 | 19 | 7 |
P value = 7.52e-05 (Fisher's exact test), Q value = 0.057
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 158 |
AMP PEAK 29(20Q13.12) MUTATED | 277 | 132 |
AMP PEAK 29(20Q13.12) WILD-TYPE | 135 | 26 |
P value = 1.44e-13 (Fisher's exact test), Q value = 1.1e-10
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
AMP PEAK 29(20Q13.12) MUTATED | 258 | 17 | 124 | 6 |
AMP PEAK 29(20Q13.12) WILD-TYPE | 98 | 37 | 18 | 7 |
P value = 0.000157 (Fisher's exact test), Q value = 0.12
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 158 |
AMP PEAK 30(20Q13.32) MUTATED | 279 | 132 |
AMP PEAK 30(20Q13.32) WILD-TYPE | 133 | 26 |
P value = 1.34e-13 (Fisher's exact test), Q value = 1e-10
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
AMP PEAK 30(20Q13.32) MUTATED | 260 | 17 | 124 | 6 |
AMP PEAK 30(20Q13.32) WILD-TYPE | 96 | 37 | 18 | 7 |
P value = 0.000257 (Fisher's exact test), Q value = 0.19
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
DEL PEAK 2(1P36.11) MUTATED | 108 | 4 | 42 | 7 |
DEL PEAK 2(1P36.11) WILD-TYPE | 248 | 50 | 100 | 6 |
P value = 0.000137 (Fisher's exact test), Q value = 0.1
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
DEL PEAK 14(4Q22.1) MUTATED | 82 | 3 | 48 | 2 |
DEL PEAK 14(4Q22.1) WILD-TYPE | 274 | 51 | 94 | 11 |
P value = 8.34e-05 (Fisher's exact test), Q value = 0.063
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
DEL PEAK 22(8P23.2) MUTATED | 144 | 11 | 78 | 6 |
DEL PEAK 22(8P23.2) WILD-TYPE | 212 | 43 | 64 | 7 |
P value = 0.000169 (Fisher's exact test), Q value = 0.13
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 327 | 140 | 103 |
DEL PEAK 22(8P23.2) MUTATED | 115 | 68 | 58 |
DEL PEAK 22(8P23.2) WILD-TYPE | 212 | 72 | 45 |
P value = 1.88e-05 (Fisher's exact test), Q value = 0.014
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
DEL PEAK 23(8P22) MUTATED | 155 | 10 | 80 | 6 |
DEL PEAK 23(8P22) WILD-TYPE | 201 | 44 | 62 | 7 |
P value = 2.41e-05 (Fisher's exact test), Q value = 0.018
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 327 | 140 | 103 |
DEL PEAK 23(8P22) MUTATED | 120 | 70 | 63 |
DEL PEAK 23(8P22) WILD-TYPE | 207 | 70 | 40 |
P value = 1.45e-05 (Fisher's exact test), Q value = 0.011
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
DEL PEAK 32(14Q11.2) MUTATED | 90 | 4 | 52 | 0 |
DEL PEAK 32(14Q11.2) WILD-TYPE | 266 | 50 | 90 | 13 |
P value = 0.000171 (Fisher's exact test), Q value = 0.13
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
DEL PEAK 35(15Q22.33) MUTATED | 92 | 5 | 55 | 4 |
DEL PEAK 35(15Q22.33) WILD-TYPE | 264 | 49 | 87 | 9 |
P value = 1.84e-07 (Fisher's exact test), Q value = 0.00014
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
DEL PEAK 38(17P12) MUTATED | 188 | 10 | 90 | 6 |
DEL PEAK 38(17P12) WILD-TYPE | 168 | 44 | 52 | 7 |
P value = 1.41e-05 (Fisher's exact test), Q value = 0.011
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 158 |
DEL PEAK 40(18P11.31) MUTATED | 200 | 109 |
DEL PEAK 40(18P11.31) WILD-TYPE | 212 | 49 |
P value = 9.2e-15 (Fisher's exact test), Q value = 7.2e-12
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
DEL PEAK 40(18P11.31) MUTATED | 193 | 6 | 104 | 5 |
DEL PEAK 40(18P11.31) WILD-TYPE | 163 | 48 | 38 | 8 |
P value = 8.03e-07 (Fisher's exact test), Q value = 0.00062
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 158 |
DEL PEAK 41(18Q12.2) MUTATED | 230 | 123 |
DEL PEAK 41(18Q12.2) WILD-TYPE | 182 | 35 |
P value = 5.73e-14 (Fisher's exact test), Q value = 4.5e-11
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
DEL PEAK 41(18Q12.2) MUTATED | 219 | 10 | 113 | 9 |
DEL PEAK 41(18Q12.2) WILD-TYPE | 137 | 44 | 29 | 4 |
P value = 4.62e-07 (Fisher's exact test), Q value = 0.00035
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 158 |
DEL PEAK 42(18Q21.2) MUTATED | 243 | 128 |
DEL PEAK 42(18Q21.2) WILD-TYPE | 169 | 30 |
P value = 6.42e-12 (Fisher's exact test), Q value = 5e-09
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
DEL PEAK 42(18Q21.2) MUTATED | 228 | 14 | 115 | 11 |
DEL PEAK 42(18Q21.2) WILD-TYPE | 128 | 40 | 27 | 2 |
P value = 4.08e-06 (Fisher's exact test), Q value = 0.0031
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 327 | 140 | 103 |
DEL PEAK 42(18Q21.2) MUTATED | 185 | 106 | 80 |
DEL PEAK 42(18Q21.2) WILD-TYPE | 142 | 34 | 23 |
P value = 9.83e-06 (Fisher's exact test), Q value = 0.0075
nPatients | COLON | RECTUM |
---|---|---|
ALL | 412 | 158 |
DEL PEAK 43(18Q22.1) MUTATED | 242 | 124 |
DEL PEAK 43(18Q22.1) WILD-TYPE | 170 | 34 |
P value = 1.25e-12 (Fisher's exact test), Q value = 9.7e-10
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA |
---|---|---|---|---|
ALL | 356 | 54 | 142 | 13 |
DEL PEAK 43(18Q22.1) MUTATED | 229 | 12 | 114 | 9 |
DEL PEAK 43(18Q22.1) WILD-TYPE | 127 | 42 | 28 | 4 |
P value = 2.06e-05 (Fisher's exact test), Q value = 0.016
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 327 | 140 | 103 |
DEL PEAK 43(18Q22.1) MUTATED | 184 | 103 | 79 |
DEL PEAK 43(18Q22.1) WILD-TYPE | 143 | 37 | 24 |
-
Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
-
Clinical data file = COADREAD.clin.merged.picked.txt
-
Number of patients = 574
-
Number of copy number variation regions = 78
-
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.