(primary solid tumor cohort)
This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 68 arm-level results and 11 clinical features across 413 patients, 34 significant findings detected with Q value < 0.25.
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Amp Peak 11(13q12.13) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Amp Peak 12(13q22.1) cnv correlated to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.
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Amp Peak 13(16p11.2) cnv correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
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Amp Peak 14(16q12.1) cnv correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
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Amp Peak 22(20q11.21) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Amp Peak 23(20q12) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Amp Peak 24(20q13.32) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Del Peak 1(1p36.11) cnv correlated to 'PATHOLOGICSPREAD(M)'.
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Del Peak 9(4p16.2) cnv correlated to 'Time to Death', 'PATHOLOGY.N', and 'PATHOLOGICSPREAD(M)'.
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Del Peak 13(5q21.3) cnv correlated to 'PATHOLOGY.N'.
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Del Peak 18(8p23.3) cnv correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
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Del Peak 19(8p22) cnv correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
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Del Peak 21(8p11.21) cnv correlated to 'PATHOLOGY.N'.
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Del Peak 28(13q14.13) cnv correlated to 'PATHOLOGICSPREAD(M)'.
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Del Peak 35(17p12) cnv correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'NUMBER.OF.LYMPH.NODES'.
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Del Peak 37(18p11.31) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Del Peak 38(18q12.2) cnv correlated to 'HISTOLOGICAL.TYPE'.
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Del Peak 39(18q21.2) cnv correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Del Peak 40(18q22.1) cnv correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
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Del Peak 41(19p13.3) cnv correlated to 'PATHOLOGY.N'.
Clinical Features |
Time to Death |
AGE | 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 | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | |
Del Peak 35(17p12) | 229 (55%) | 184 |
0.334 (1.00) |
0.0108 (1.00) |
0.43 (1.00) |
3.38e-06 (0.0025) |
0.869 (1.00) |
2.64e-05 (0.0193) |
0.0165 (1.00) |
1.19e-06 (0.000883) |
0.257 (1.00) |
0.209 (1.00) |
6.46e-05 (0.047) |
Del Peak 9(4p16 2) | 121 (29%) | 292 |
0.00024 (0.173) |
0.609 (1.00) |
0.59 (1.00) |
0.036 (1.00) |
0.67 (1.00) |
0.000256 (0.184) |
0.000266 (0.191) |
0.000587 (0.414) |
0.0247 (1.00) |
0.0291 (1.00) |
0.0076 (1.00) |
Del Peak 39(18q21 2) | 260 (63%) | 153 |
0.4 (1.00) |
0.0992 (1.00) |
0.127 (1.00) |
3.87e-09 (2.88e-06) |
0.805 (1.00) |
0.000112 (0.081) |
0.00624 (1.00) |
9.14e-06 (0.00672) |
0.299 (1.00) |
0.155 (1.00) |
0.0205 (1.00) |
Del Peak 40(18q22 1) | 260 (63%) | 153 |
0.263 (1.00) |
0.176 (1.00) |
0.127 (1.00) |
4.48e-10 (3.34e-07) |
0.805 (1.00) |
0.000112 (0.081) |
0.00624 (1.00) |
2.02e-05 (0.0148) |
0.299 (1.00) |
0.269 (1.00) |
0.0265 (1.00) |
Amp Peak 12(13q22 1) | 254 (62%) | 159 |
0.0716 (1.00) |
0.565 (1.00) |
0.363 (1.00) |
8.13e-06 (0.00599) |
1 (1.00) |
0.00143 (0.988) |
0.00698 (1.00) |
0.000315 (0.226) |
0.288 (1.00) |
0.077 (1.00) |
0.0816 (1.00) |
Amp Peak 13(16p11 2) | 116 (28%) | 297 |
0.426 (1.00) |
0.0688 (1.00) |
0.584 (1.00) |
0.00867 (1.00) |
0.48 (1.00) |
0.000142 (0.102) |
0.323 (1.00) |
0.000162 (0.117) |
1 (1.00) |
0.867 (1.00) |
0.00552 (1.00) |
Amp Peak 14(16q12 1) | 102 (25%) | 311 |
0.356 (1.00) |
0.0166 (1.00) |
0.493 (1.00) |
0.0112 (1.00) |
0.947 (1.00) |
0.000185 (0.133) |
0.18 (1.00) |
3e-05 (0.022) |
0.574 (1.00) |
0.812 (1.00) |
0.0162 (1.00) |
Del Peak 18(8p23 3) | 171 (41%) | 242 |
0.566 (1.00) |
0.251 (1.00) |
0.193 (1.00) |
0.0746 (1.00) |
0.165 (1.00) |
0.000318 (0.227) |
0.0225 (1.00) |
9.26e-05 (0.0673) |
0.572 (1.00) |
0.0397 (1.00) |
0.00532 (1.00) |
Del Peak 19(8p22) | 185 (45%) | 228 |
0.433 (1.00) |
0.104 (1.00) |
0.321 (1.00) |
0.0185 (1.00) |
0.222 (1.00) |
7.69e-06 (0.00567) |
0.00136 (0.946) |
2.17e-07 (0.000161) |
0.589 (1.00) |
0.0225 (1.00) |
0.00105 (0.732) |
Amp Peak 11(13q12 13) | 250 (61%) | 163 |
0.29 (1.00) |
0.522 (1.00) |
0.92 (1.00) |
8.87e-07 (0.000659) |
0.966 (1.00) |
0.00311 (1.00) |
0.00471 (1.00) |
0.000464 (0.33) |
0.282 (1.00) |
0.0373 (1.00) |
0.0534 (1.00) |
Amp Peak 22(20q11 21) | 296 (72%) | 117 |
0.433 (1.00) |
0.474 (1.00) |
0.382 (1.00) |
7.66e-06 (0.00566) |
0.542 (1.00) |
0.0243 (1.00) |
0.0102 (1.00) |
0.000866 (0.61) |
0.562 (1.00) |
0.132 (1.00) |
0.0736 (1.00) |
Amp Peak 23(20q12) | 297 (72%) | 116 |
0.365 (1.00) |
0.51 (1.00) |
0.324 (1.00) |
1.38e-06 (0.00102) |
0.678 (1.00) |
0.0293 (1.00) |
0.00474 (1.00) |
0.000579 (0.41) |
0.563 (1.00) |
0.134 (1.00) |
0.0994 (1.00) |
Amp Peak 24(20q13 32) | 300 (73%) | 113 |
0.371 (1.00) |
0.537 (1.00) |
0.377 (1.00) |
4.8e-06 (0.00355) |
0.631 (1.00) |
0.0182 (1.00) |
0.00667 (1.00) |
0.000567 (0.402) |
0.565 (1.00) |
0.138 (1.00) |
0.0271 (1.00) |
Del Peak 1(1p36 11) | 150 (36%) | 263 |
0.0209 (1.00) |
0.144 (1.00) |
0.54 (1.00) |
0.00362 (1.00) |
0.653 (1.00) |
0.00498 (1.00) |
0.000122 (0.0881) |
0.000885 (0.622) |
1 (1.00) |
0.0322 (1.00) |
0.0061 (1.00) |
Del Peak 13(5q21 3) | 117 (28%) | 296 |
0.0728 (1.00) |
0.0679 (1.00) |
0.743 (1.00) |
0.196 (1.00) |
0.976 (1.00) |
5.3e-05 (0.0387) |
0.0201 (1.00) |
0.000579 (0.41) |
0.0223 (1.00) |
0.0902 (1.00) |
0.00516 (1.00) |
Del Peak 21(8p11 21) | 43 (10%) | 370 |
0.826 (1.00) |
0.377 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.155 (1.00) |
0.000316 (0.226) |
0.00793 (1.00) |
0.00102 (0.714) |
0.282 (1.00) |
0.121 (1.00) |
0.0181 (1.00) |
Del Peak 28(13q14 13) | 18 (4%) | 395 |
0.312 (1.00) |
0.279 (1.00) |
1 (1.00) |
1 (1.00) |
0.719 (1.00) |
0.0629 (1.00) |
4.33e-05 (0.0316) |
0.835 (1.00) |
1 (1.00) |
0.726 (1.00) |
0.223 (1.00) |
Del Peak 37(18p11 31) | 220 (53%) | 193 |
0.869 (1.00) |
0.0199 (1.00) |
1 (1.00) |
8.39e-11 (6.28e-08) |
0.819 (1.00) |
0.0479 (1.00) |
0.00385 (1.00) |
0.00181 (1.00) |
0.251 (1.00) |
0.0655 (1.00) |
0.375 (1.00) |
Del Peak 38(18q12 2) | 247 (60%) | 166 |
0.983 (1.00) |
0.0542 (1.00) |
0.421 (1.00) |
3.02e-10 (2.25e-07) |
0.838 (1.00) |
0.002 (1.00) |
0.0125 (1.00) |
0.000376 (0.268) |
0.277 (1.00) |
0.149 (1.00) |
0.087 (1.00) |
Del Peak 41(19p13 3) | 57 (14%) | 356 |
0.367 (1.00) |
0.148 (1.00) |
0.67 (1.00) |
0.202 (1.00) |
0.956 (1.00) |
5.85e-05 (0.0426) |
0.0321 (1.00) |
0.00168 (1.00) |
0.36 (1.00) |
0.0219 (1.00) |
0.00169 (1.00) |
Amp Peak 1(2q33 1) | 79 (19%) | 334 |
0.0421 (1.00) |
0.358 (1.00) |
0.259 (1.00) |
0.267 (1.00) |
0.834 (1.00) |
0.0212 (1.00) |
0.639 (1.00) |
0.0501 (1.00) |
0.472 (1.00) |
0.119 (1.00) |
0.0758 (1.00) |
Amp Peak 2(5p13 2) | 81 (20%) | 332 |
0.344 (1.00) |
0.234 (1.00) |
0.322 (1.00) |
0.856 (1.00) |
0.521 (1.00) |
0.034 (1.00) |
0.729 (1.00) |
0.771 (1.00) |
1 (1.00) |
0.209 (1.00) |
0.0458 (1.00) |
Amp Peak 3(5q22 3) | 40 (10%) | 373 |
0.975 (1.00) |
0.768 (1.00) |
0.74 (1.00) |
0.332 (1.00) |
0.781 (1.00) |
0.201 (1.00) |
0.00941 (1.00) |
0.0736 (1.00) |
0.264 (1.00) |
0.0908 (1.00) |
0.266 (1.00) |
Amp Peak 4(6p21 1) | 89 (22%) | 324 |
0.855 (1.00) |
0.829 (1.00) |
0.283 (1.00) |
0.0505 (1.00) |
0.568 (1.00) |
0.00138 (0.957) |
0.609 (1.00) |
0.0106 (1.00) |
0.00974 (1.00) |
0.254 (1.00) |
0.013 (1.00) |
Amp Peak 5(8p11 23) | 144 (35%) | 269 |
0.875 (1.00) |
0.293 (1.00) |
0.757 (1.00) |
0.168 (1.00) |
0.791 (1.00) |
0.721 (1.00) |
0.569 (1.00) |
0.928 (1.00) |
0.279 (1.00) |
0.434 (1.00) |
0.856 (1.00) |
Amp Peak 6(8p11 21) | 173 (42%) | 240 |
0.419 (1.00) |
0.449 (1.00) |
0.272 (1.00) |
0.184 (1.00) |
0.765 (1.00) |
0.556 (1.00) |
0.466 (1.00) |
0.958 (1.00) |
0.574 (1.00) |
0.501 (1.00) |
0.867 (1.00) |
Amp Peak 7(8q12 1) | 215 (52%) | 198 |
0.858 (1.00) |
0.113 (1.00) |
0.844 (1.00) |
0.0189 (1.00) |
0.417 (1.00) |
0.362 (1.00) |
0.158 (1.00) |
0.394 (1.00) |
0.249 (1.00) |
0.341 (1.00) |
0.0598 (1.00) |
Amp Peak 8(8q24 21) | 239 (58%) | 174 |
0.637 (1.00) |
0.074 (1.00) |
0.485 (1.00) |
0.0753 (1.00) |
0.2 (1.00) |
0.282 (1.00) |
0.0847 (1.00) |
0.25 (1.00) |
0.267 (1.00) |
0.375 (1.00) |
0.0494 (1.00) |
Amp Peak 9(11p15 5) | 86 (21%) | 327 |
0.603 (1.00) |
0.0407 (1.00) |
0.544 (1.00) |
0.00194 (1.00) |
0.151 (1.00) |
0.276 (1.00) |
0.254 (1.00) |
0.154 (1.00) |
0.111 (1.00) |
0.212 (1.00) |
0.265 (1.00) |
Amp Peak 10(12p13 33) | 104 (25%) | 309 |
0.2 (1.00) |
0.139 (1.00) |
0.734 (1.00) |
0.501 (1.00) |
0.16 (1.00) |
0.144 (1.00) |
0.2 (1.00) |
0.112 (1.00) |
0.575 (1.00) |
0.519 (1.00) |
0.829 (1.00) |
Amp Peak 15(17q12) | 101 (24%) | 312 |
0.479 (1.00) |
0.45 (1.00) |
0.252 (1.00) |
0.313 (1.00) |
0.25 (1.00) |
0.113 (1.00) |
0.0126 (1.00) |
0.0172 (1.00) |
0.57 (1.00) |
0.112 (1.00) |
0.144 (1.00) |
Amp Peak 16(17q24 1) | 92 (22%) | 321 |
0.076 (1.00) |
0.414 (1.00) |
0.638 (1.00) |
0.112 (1.00) |
0.409 (1.00) |
0.341 (1.00) |
0.0351 (1.00) |
0.21 (1.00) |
0.531 (1.00) |
0.205 (1.00) |
0.961 (1.00) |
Amp Peak 17(19p13 2) | 65 (16%) | 348 |
0.63 (1.00) |
0.618 (1.00) |
0.0575 (1.00) |
0.228 (1.00) |
0.655 (1.00) |
0.0194 (1.00) |
0.00672 (1.00) |
0.231 (1.00) |
0.403 (1.00) |
0.137 (1.00) |
0.354 (1.00) |
Amp Peak 18(19q13 11) | 83 (20%) | 330 |
0.201 (1.00) |
0.68 (1.00) |
0.0648 (1.00) |
0.364 (1.00) |
0.942 (1.00) |
0.129 (1.00) |
0.0224 (1.00) |
0.486 (1.00) |
0.491 (1.00) |
0.686 (1.00) |
0.966 (1.00) |
Amp Peak 19(20p12 3) | 184 (45%) | 229 |
0.0533 (1.00) |
0.491 (1.00) |
0.197 (1.00) |
0.0554 (1.00) |
0.962 (1.00) |
0.0795 (1.00) |
0.00371 (1.00) |
0.00697 (1.00) |
0.0876 (1.00) |
0.0245 (1.00) |
0.0123 (1.00) |
Amp Peak 20(20p11 23) | 205 (50%) | 208 |
0.234 (1.00) |
0.974 (1.00) |
0.2 (1.00) |
0.0127 (1.00) |
0.947 (1.00) |
0.0614 (1.00) |
0.00206 (1.00) |
0.00876 (1.00) |
0.121 (1.00) |
0.0242 (1.00) |
0.124 (1.00) |
Amp Peak 21(20p11 21) | 230 (56%) | 183 |
0.453 (1.00) |
0.466 (1.00) |
0.165 (1.00) |
0.00494 (1.00) |
0.897 (1.00) |
0.272 (1.00) |
0.00305 (1.00) |
0.0131 (1.00) |
0.258 (1.00) |
0.0488 (1.00) |
0.323 (1.00) |
Del Peak 2(1p33) | 107 (26%) | 306 |
0.00122 (0.848) |
0.89 (1.00) |
0.91 (1.00) |
0.132 (1.00) |
0.505 (1.00) |
0.00466 (1.00) |
0.00786 (1.00) |
0.0144 (1.00) |
0.572 (1.00) |
0.0993 (1.00) |
0.0145 (1.00) |
Del Peak 3(1p13 1) | 103 (25%) | 310 |
0.0503 (1.00) |
0.891 (1.00) |
0.496 (1.00) |
0.133 (1.00) |
0.541 (1.00) |
0.00105 (0.733) |
0.000797 (0.562) |
0.00869 (1.00) |
1 (1.00) |
0.0566 (1.00) |
0.00935 (1.00) |
Del Peak 4(1q43) | 44 (11%) | 369 |
0.488 (1.00) |
0.525 (1.00) |
0.875 (1.00) |
0.818 (1.00) |
0.3 (1.00) |
0.179 (1.00) |
0.077 (1.00) |
0.158 (1.00) |
0.287 (1.00) |
0.0922 (1.00) |
0.291 (1.00) |
Del Peak 5(2q37 2) | 21 (5%) | 392 |
0.368 (1.00) |
0.447 (1.00) |
0.374 (1.00) |
0.748 (1.00) |
0.447 (1.00) |
0.825 (1.00) |
0.361 (1.00) |
0.454 (1.00) |
1 (1.00) |
1 (1.00) |
0.168 (1.00) |
Del Peak 6(3p26 1) | 60 (15%) | 353 |
0.000411 (0.293) |
0.346 (1.00) |
1 (1.00) |
0.146 (1.00) |
0.0583 (1.00) |
0.0186 (1.00) |
0.000457 (0.325) |
0.000553 (0.393) |
1 (1.00) |
0.0726 (1.00) |
0.177 (1.00) |
Del Peak 7(3p14 2) | 75 (18%) | 338 |
0.426 (1.00) |
0.608 (1.00) |
0.371 (1.00) |
0.186 (1.00) |
0.189 (1.00) |
0.0486 (1.00) |
0.0569 (1.00) |
0.0529 (1.00) |
1 (1.00) |
0.123 (1.00) |
0.0322 (1.00) |
Del Peak 8(3q26 31) | 39 (9%) | 374 |
0.452 (1.00) |
0.85 (1.00) |
1 (1.00) |
0.14 (1.00) |
0.0989 (1.00) |
0.595 (1.00) |
0.619 (1.00) |
0.168 (1.00) |
1 (1.00) |
0.599 (1.00) |
0.374 (1.00) |
Del Peak 10(4q22 1) | 126 (31%) | 287 |
0.009 (1.00) |
0.967 (1.00) |
0.593 (1.00) |
0.0174 (1.00) |
0.341 (1.00) |
0.00186 (1.00) |
0.118 (1.00) |
0.0169 (1.00) |
0.0279 (1.00) |
0.436 (1.00) |
0.0153 (1.00) |
Del Peak 11(4q35 1) | 137 (33%) | 276 |
0.0437 (1.00) |
0.255 (1.00) |
0.249 (1.00) |
0.0871 (1.00) |
0.72 (1.00) |
0.00586 (1.00) |
0.221 (1.00) |
0.0424 (1.00) |
0.036 (1.00) |
0.14 (1.00) |
0.0635 (1.00) |
Del Peak 12(5q11 2) | 91 (22%) | 322 |
0.0477 (1.00) |
0.0453 (1.00) |
0.408 (1.00) |
0.112 (1.00) |
0.899 (1.00) |
0.00319 (1.00) |
0.0574 (1.00) |
0.00895 (1.00) |
0.124 (1.00) |
0.269 (1.00) |
0.0149 (1.00) |
Del Peak 14(5q23 1) | 107 (26%) | 306 |
0.129 (1.00) |
0.285 (1.00) |
0.311 (1.00) |
0.0983 (1.00) |
0.946 (1.00) |
0.00593 (1.00) |
0.0116 (1.00) |
0.0366 (1.00) |
0.017 (1.00) |
0.109 (1.00) |
0.0287 (1.00) |
Del Peak 15(6p25 3) | 54 (13%) | 359 |
0.704 (1.00) |
0.0948 (1.00) |
0.0794 (1.00) |
0.516 (1.00) |
0.126 (1.00) |
0.932 (1.00) |
0.18 (1.00) |
0.825 (1.00) |
1 (1.00) |
0.297 (1.00) |
0.738 (1.00) |
Del Peak 16(6q26) | 60 (15%) | 353 |
0.0205 (1.00) |
0.928 (1.00) |
0.782 (1.00) |
1 (1.00) |
0.194 (1.00) |
0.0248 (1.00) |
0.0212 (1.00) |
0.11 (1.00) |
1 (1.00) |
0.0169 (1.00) |
0.0144 (1.00) |
Del Peak 17(7q31 1) | 11 (3%) | 402 |
0.978 (1.00) |
0.589 (1.00) |
0.36 (1.00) |
1 (1.00) |
0.571 (1.00) |
1 (1.00) |
0.498 (1.00) |
0.493 (1.00) |
1 (1.00) |
1 (1.00) |
0.666 (1.00) |
Del Peak 20(8p11 22) | 80 (19%) | 333 |
0.412 (1.00) |
0.236 (1.00) |
0.803 (1.00) |
0.461 (1.00) |
0.342 (1.00) |
0.000914 (0.642) |
0.0887 (1.00) |
0.00266 (1.00) |
0.0973 (1.00) |
0.248 (1.00) |
0.0333 (1.00) |
Del Peak 22(9p21 3) | 56 (14%) | 357 |
0.0248 (1.00) |
0.0603 (1.00) |
0.251 (1.00) |
0.202 (1.00) |
0.292 (1.00) |
0.144 (1.00) |
0.106 (1.00) |
0.399 (1.00) |
1 (1.00) |
0.272 (1.00) |
0.309 (1.00) |
Del Peak 23(10p15 3) | 68 (16%) | 345 |
0.847 (1.00) |
0.434 (1.00) |
0.791 (1.00) |
0.557 (1.00) |
0.856 (1.00) |
0.00164 (1.00) |
0.00231 (1.00) |
0.0011 (0.765) |
0.0717 (1.00) |
0.547 (1.00) |
0.0712 (1.00) |
Del Peak 24(10q21 1) | 82 (20%) | 331 |
0.959 (1.00) |
0.0528 (1.00) |
0.388 (1.00) |
0.0995 (1.00) |
0.952 (1.00) |
0.00851 (1.00) |
0.0976 (1.00) |
0.0196 (1.00) |
0.102 (1.00) |
0.0115 (1.00) |
0.0801 (1.00) |
Del Peak 25(10q23 31) | 94 (23%) | 319 |
0.834 (1.00) |
0.0124 (1.00) |
0.483 (1.00) |
0.164 (1.00) |
0.503 (1.00) |
0.00523 (1.00) |
0.00814 (1.00) |
0.0221 (1.00) |
0.131 (1.00) |
0.0496 (1.00) |
0.0907 (1.00) |
Del Peak 26(10q25 2) | 93 (23%) | 320 |
0.313 (1.00) |
0.164 (1.00) |
0.907 (1.00) |
0.164 (1.00) |
0.227 (1.00) |
0.00365 (1.00) |
0.0681 (1.00) |
0.0169 (1.00) |
0.129 (1.00) |
0.0132 (1.00) |
0.0781 (1.00) |
Del Peak 27(12p13 2) | 44 (11%) | 369 |
0.384 (1.00) |
0.633 (1.00) |
0.338 (1.00) |
0.00188 (1.00) |
0.897 (1.00) |
0.0822 (1.00) |
0.166 (1.00) |
0.0971 (1.00) |
1 (1.00) |
0.619 (1.00) |
0.697 (1.00) |
Del Peak 29(14q32 11) | 133 (32%) | 280 |
0.353 (1.00) |
0.506 (1.00) |
0.674 (1.00) |
0.000917 (0.643) |
0.631 (1.00) |
0.0613 (1.00) |
0.0367 (1.00) |
0.00434 (1.00) |
0.554 (1.00) |
0.326 (1.00) |
0.136 (1.00) |
Del Peak 30(15q11 2) | 160 (39%) | 253 |
0.93 (1.00) |
0.852 (1.00) |
1 (1.00) |
0.0238 (1.00) |
0.912 (1.00) |
0.0115 (1.00) |
0.0635 (1.00) |
0.00321 (1.00) |
0.0575 (1.00) |
0.321 (1.00) |
0.252 (1.00) |
Del Peak 31(15q21 1) | 151 (37%) | 262 |
0.0937 (1.00) |
0.658 (1.00) |
0.919 (1.00) |
0.0488 (1.00) |
0.965 (1.00) |
0.0824 (1.00) |
0.0887 (1.00) |
0.0559 (1.00) |
0.0483 (1.00) |
0.547 (1.00) |
0.467 (1.00) |
Del Peak 32(15q22 33) | 145 (35%) | 268 |
0.255 (1.00) |
0.426 (1.00) |
0.918 (1.00) |
0.00592 (1.00) |
0.58 (1.00) |
0.0403 (1.00) |
0.0478 (1.00) |
0.0218 (1.00) |
0.0427 (1.00) |
0.511 (1.00) |
0.33 (1.00) |
Del Peak 33(16p13 3) | 45 (11%) | 368 |
0.00179 (1.00) |
0.426 (1.00) |
0.755 (1.00) |
1 (1.00) |
0.0362 (1.00) |
0.0647 (1.00) |
0.357 (1.00) |
0.163 (1.00) |
1 (1.00) |
0.724 (1.00) |
0.109 (1.00) |
Del Peak 34(16q23 1) | 49 (12%) | 364 |
0.00129 (0.894) |
0.288 (1.00) |
0.129 (1.00) |
0.261 (1.00) |
0.631 (1.00) |
0.384 (1.00) |
0.979 (1.00) |
0.896 (1.00) |
1 (1.00) |
0.872 (1.00) |
0.26 (1.00) |
Del Peak 36(17q24 3) | 59 (14%) | 354 |
0.729 (1.00) |
0.51 (1.00) |
0.328 (1.00) |
1 (1.00) |
0.687 (1.00) |
0.00836 (1.00) |
0.253 (1.00) |
0.0329 (1.00) |
1 (1.00) |
0.255 (1.00) |
0.0379 (1.00) |
Del Peak 42(20p12 1) | 79 (19%) | 334 |
0.803 (1.00) |
0.439 (1.00) |
0.618 (1.00) |
0.137 (1.00) |
0.695 (1.00) |
0.553 (1.00) |
0.983 (1.00) |
0.419 (1.00) |
1 (1.00) |
0.686 (1.00) |
0.531 (1.00) |
Del Peak 43(21q11 2) | 125 (30%) | 288 |
0.468 (1.00) |
0.722 (1.00) |
1 (1.00) |
0.0101 (1.00) |
0.267 (1.00) |
0.0417 (1.00) |
0.344 (1.00) |
0.187 (1.00) |
0.219 (1.00) |
0.395 (1.00) |
0.0108 (1.00) |
Del Peak 44(22q13 32) | 138 (33%) | 275 |
0.208 (1.00) |
0.701 (1.00) |
0.603 (1.00) |
0.00499 (1.00) |
0.732 (1.00) |
0.00257 (1.00) |
0.0348 (1.00) |
0.014 (1.00) |
1 (1.00) |
0.239 (1.00) |
0.00975 (1.00) |
P value = 8.87e-07 (Fisher's exact test), Q value = 0.00066
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
AMP PEAK 11(13Q12.13) MUTATED | 233 | 16 |
AMP PEAK 11(13Q12.13) WILD-TYPE | 123 | 38 |
P value = 8.13e-06 (Fisher's exact test), Q value = 0.006
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
AMP PEAK 12(13Q22.1) MUTATED | 235 | 18 |
AMP PEAK 12(13Q22.1) WILD-TYPE | 121 | 36 |
P value = 0.000315 (Fisher's exact test), Q value = 0.23
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 67 | 157 | 116 | 56 |
AMP PEAK 12(13Q22.1) MUTATED | 40 | 79 | 78 | 45 |
AMP PEAK 12(13Q22.1) WILD-TYPE | 27 | 78 | 38 | 11 |
P value = 0.000142 (Fisher's exact test), Q value = 0.1
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
AMP PEAK 13(16P11.2) MUTATED | 50 | 35 | 30 |
AMP PEAK 13(16P11.2) WILD-TYPE | 195 | 60 | 41 |
P value = 0.000162 (Fisher's exact test), Q value = 0.12
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 67 | 157 | 116 | 56 |
AMP PEAK 13(16P11.2) MUTATED | 12 | 30 | 48 | 18 |
AMP PEAK 13(16P11.2) WILD-TYPE | 55 | 127 | 68 | 38 |
P value = 0.000185 (Fisher's exact test), Q value = 0.13
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
AMP PEAK 14(16Q12.1) MUTATED | 43 | 33 | 26 |
AMP PEAK 14(16Q12.1) WILD-TYPE | 202 | 62 | 45 |
P value = 3e-05 (Fisher's exact test), Q value = 0.022
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 67 | 157 | 116 | 56 |
AMP PEAK 14(16Q12.1) MUTATED | 12 | 23 | 46 | 14 |
AMP PEAK 14(16Q12.1) WILD-TYPE | 55 | 134 | 70 | 42 |
P value = 7.66e-06 (Fisher's exact test), Q value = 0.0057
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
AMP PEAK 22(20Q11.21) MUTATED | 269 | 24 |
AMP PEAK 22(20Q11.21) WILD-TYPE | 87 | 30 |
P value = 1.38e-06 (Fisher's exact test), Q value = 0.001
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
AMP PEAK 23(20Q12) MUTATED | 271 | 23 |
AMP PEAK 23(20Q12) WILD-TYPE | 85 | 31 |
P value = 4.8e-06 (Fisher's exact test), Q value = 0.0035
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
AMP PEAK 24(20Q13.32) MUTATED | 273 | 24 |
AMP PEAK 24(20Q13.32) WILD-TYPE | 83 | 30 |
P value = 0.000122 (Chi-square test), Q value = 0.088
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 312 | 49 | 7 | 1 | 36 |
DEL PEAK 1(1P36.11) MUTATED | 101 | 33 | 2 | 0 | 13 |
DEL PEAK 1(1P36.11) WILD-TYPE | 211 | 16 | 5 | 1 | 23 |
P value = 0.00024 (logrank test), Q value = 0.17
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 319 | 49 | 0.1 - 135.5 (7.7) |
DEL PEAK 9(4P16.2) MUTATED | 89 | 20 | 0.2 - 87.8 (7.6) |
DEL PEAK 9(4P16.2) WILD-TYPE | 230 | 29 | 0.1 - 135.5 (8.0) |
P value = 0.000256 (Fisher's exact test), Q value = 0.18
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
DEL PEAK 9(4P16.2) MUTATED | 54 | 34 | 32 |
DEL PEAK 9(4P16.2) WILD-TYPE | 191 | 61 | 39 |
P value = 0.000266 (Chi-square test), Q value = 0.19
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 312 | 49 | 7 | 1 | 36 |
DEL PEAK 9(4P16.2) MUTATED | 75 | 27 | 3 | 0 | 12 |
DEL PEAK 9(4P16.2) WILD-TYPE | 237 | 22 | 4 | 1 | 24 |
P value = 5.3e-05 (Fisher's exact test), Q value = 0.039
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
DEL PEAK 13(5Q21.3) MUTATED | 50 | 34 | 32 |
DEL PEAK 13(5Q21.3) WILD-TYPE | 195 | 61 | 39 |
P value = 0.000318 (Fisher's exact test), Q value = 0.23
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
DEL PEAK 18(8P23.3) MUTATED | 82 | 46 | 41 |
DEL PEAK 18(8P23.3) WILD-TYPE | 163 | 49 | 30 |
P value = 9.26e-05 (Fisher's exact test), Q value = 0.067
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 67 | 157 | 116 | 56 |
DEL PEAK 18(8P23.3) MUTATED | 24 | 48 | 59 | 34 |
DEL PEAK 18(8P23.3) WILD-TYPE | 43 | 109 | 57 | 22 |
P value = 7.69e-06 (Fisher's exact test), Q value = 0.0057
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
DEL PEAK 19(8P22) MUTATED | 87 | 49 | 47 |
DEL PEAK 19(8P22) WILD-TYPE | 158 | 46 | 24 |
P value = 2.17e-07 (Fisher's exact test), Q value = 0.00016
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 67 | 157 | 116 | 56 |
DEL PEAK 19(8P22) MUTATED | 24 | 50 | 66 | 39 |
DEL PEAK 19(8P22) WILD-TYPE | 43 | 107 | 50 | 17 |
P value = 0.000316 (Fisher's exact test), Q value = 0.23
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
DEL PEAK 21(8P11.21) MUTATED | 14 | 14 | 15 |
DEL PEAK 21(8P11.21) WILD-TYPE | 231 | 81 | 56 |
P value = 4.33e-05 (Chi-square test), Q value = 0.032
nPatients | M0 | M1 | M1A | M1B | MX |
---|---|---|---|---|---|
ALL | 312 | 49 | 7 | 1 | 36 |
DEL PEAK 28(13Q14.13) MUTATED | 12 | 1 | 0 | 1 | 2 |
DEL PEAK 28(13Q14.13) WILD-TYPE | 300 | 48 | 7 | 0 | 34 |
P value = 3.38e-06 (Fisher's exact test), Q value = 0.0025
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
DEL PEAK 35(17P12) MUTATED | 213 | 14 |
DEL PEAK 35(17P12) WILD-TYPE | 143 | 40 |
P value = 2.64e-05 (Fisher's exact test), Q value = 0.019
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
DEL PEAK 35(17P12) MUTATED | 113 | 63 | 51 |
DEL PEAK 35(17P12) WILD-TYPE | 132 | 32 | 20 |
P value = 1.19e-06 (Fisher's exact test), Q value = 0.00088
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 67 | 157 | 116 | 56 |
DEL PEAK 35(17P12) MUTATED | 34 | 64 | 80 | 41 |
DEL PEAK 35(17P12) WILD-TYPE | 33 | 93 | 36 | 15 |
P value = 6.46e-05 (t-test), Q value = 0.047
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 389 | 2.0 (4.5) |
DEL PEAK 35(17P12) MUTATED | 216 | 2.8 (5.5) |
DEL PEAK 35(17P12) WILD-TYPE | 173 | 1.1 (2.4) |
P value = 8.39e-11 (Fisher's exact test), Q value = 6.3e-08
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
DEL PEAK 37(18P11.31) MUTATED | 211 | 7 |
DEL PEAK 37(18P11.31) WILD-TYPE | 145 | 47 |
P value = 3.02e-10 (Fisher's exact test), Q value = 2.3e-07
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
DEL PEAK 38(18Q12.2) MUTATED | 235 | 11 |
DEL PEAK 38(18Q12.2) WILD-TYPE | 121 | 43 |
P value = 3.87e-09 (Fisher's exact test), Q value = 2.9e-06
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
DEL PEAK 39(18Q21.2) MUTATED | 245 | 14 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 111 | 40 |
P value = 0.000112 (Fisher's exact test), Q value = 0.081
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
DEL PEAK 39(18Q21.2) MUTATED | 134 | 68 | 56 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 111 | 27 | 15 |
P value = 9.14e-06 (Fisher's exact test), Q value = 0.0067
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 67 | 157 | 116 | 56 |
DEL PEAK 39(18Q21.2) MUTATED | 36 | 81 | 83 | 47 |
DEL PEAK 39(18Q21.2) WILD-TYPE | 31 | 76 | 33 | 9 |
P value = 4.48e-10 (Fisher's exact test), Q value = 3.3e-07
nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA |
---|---|---|
ALL | 356 | 54 |
DEL PEAK 40(18Q22.1) MUTATED | 246 | 13 |
DEL PEAK 40(18Q22.1) WILD-TYPE | 110 | 41 |
P value = 0.000112 (Fisher's exact test), Q value = 0.081
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
DEL PEAK 40(18Q22.1) MUTATED | 134 | 68 | 56 |
DEL PEAK 40(18Q22.1) WILD-TYPE | 111 | 27 | 15 |
P value = 2.02e-05 (Fisher's exact test), Q value = 0.015
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 67 | 157 | 116 | 56 |
DEL PEAK 40(18Q22.1) MUTATED | 36 | 82 | 82 | 47 |
DEL PEAK 40(18Q22.1) WILD-TYPE | 31 | 75 | 34 | 9 |
P value = 5.85e-05 (Fisher's exact test), Q value = 0.043
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 245 | 95 | 71 |
DEL PEAK 41(19P13.3) MUTATED | 22 | 13 | 22 |
DEL PEAK 41(19P13.3) WILD-TYPE | 223 | 82 | 49 |
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = COAD-TP.clin.merged.picked.txt
-
Number of patients = 413
-
Number of significantly arm-level cnvs = 68
-
Number of selected clinical features = 11
-
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.