Stomach Adenocarcinoma: Correlation between copy number variation genes (focal) and selected clinical features
(primary solid tumor cohort)
(primary solid tumor cohort)
Maintained by TCGA GDAC Team
(Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction
This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Summary
Testing the association between copy number variation 75 arm-level results and 11 clinical features across 177 patients, one significant finding detected with Q value < 0.25.
-
Del Peak 22(10q23.31) cnv correlated to 'PATHOLOGY.T'.
Results
Overview of the results
Table 1. Get Full Table Overview of the association between significant copy number variation of 75 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.
|
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 | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | |
| Del Peak 22(10q23 31) | 38 (21%) | 139 |
0.332 (1.00) |
0.0735 (1.00) |
0.349 (1.00) |
0.126 (1.00) |
0.000181 (0.149) |
0.85 (1.00) |
0.82 (1.00) |
0.53 (1.00) |
1 (1.00) |
0.936 (1.00) |
0.143 (1.00) |
| Amp Peak 1(1p36 22) | 24 (14%) | 153 |
0.427 (1.00) |
0.995 (1.00) |
0.0464 (1.00) |
0.159 (1.00) |
0.173 (1.00) |
0.382 (1.00) |
0.347 (1.00) |
0.251 (1.00) |
0.522 (1.00) |
0.628 (1.00) |
0.44 (1.00) |
| Amp Peak 2(1q21 3) | 55 (31%) | 122 |
0.996 (1.00) |
0.0964 (1.00) |
0.869 (1.00) |
0.151 (1.00) |
0.192 (1.00) |
0.335 (1.00) |
0.211 (1.00) |
0.749 (1.00) |
0.033 (1.00) |
0.387 (1.00) |
0.0823 (1.00) |
| Amp Peak 3(1q42 3) | 53 (30%) | 124 |
0.838 (1.00) |
0.687 (1.00) |
0.24 (1.00) |
0.0239 (1.00) |
0.621 (1.00) |
0.647 (1.00) |
0.167 (1.00) |
0.662 (1.00) |
0.159 (1.00) |
0.911 (1.00) |
0.457 (1.00) |
| Amp Peak 4(3q26 2) | 50 (28%) | 127 |
0.873 (1.00) |
0.546 (1.00) |
0.125 (1.00) |
0.0778 (1.00) |
0.573 (1.00) |
0.896 (1.00) |
0.0176 (1.00) |
0.735 (1.00) |
1 (1.00) |
0.636 (1.00) |
0.693 (1.00) |
| Amp Peak 5(5p15 33) | 46 (26%) | 131 |
0.781 (1.00) |
0.0617 (1.00) |
0.0807 (1.00) |
0.0466 (1.00) |
0.0241 (1.00) |
0.665 (1.00) |
1 (1.00) |
0.0923 (1.00) |
0.111 (1.00) |
0.553 (1.00) |
0.159 (1.00) |
| Amp Peak 6(5p13 1) | 44 (25%) | 133 |
0.792 (1.00) |
0.125 (1.00) |
0.0747 (1.00) |
0.671 (1.00) |
0.215 (1.00) |
0.24 (1.00) |
0.547 (1.00) |
0.0172 (1.00) |
0.099 (1.00) |
0.304 (1.00) |
0.274 (1.00) |
| Amp Peak 7(6p21 1) | 47 (27%) | 130 |
0.0141 (1.00) |
0.15 (1.00) |
0.39 (1.00) |
0.236 (1.00) |
0.00704 (1.00) |
0.697 (1.00) |
0.0939 (1.00) |
0.245 (1.00) |
0.117 (1.00) |
0.126 (1.00) |
0.373 (1.00) |
| Amp Peak 8(6q12) | 36 (20%) | 141 |
0.815 (1.00) |
0.751 (1.00) |
1 (1.00) |
0.56 (1.00) |
0.278 (1.00) |
0.803 (1.00) |
0.583 (1.00) |
0.894 (1.00) |
0.269 (1.00) |
0.266 (1.00) |
0.0786 (1.00) |
| Amp Peak 9(6q21) | 30 (17%) | 147 |
0.92 (1.00) |
0.918 (1.00) |
1 (1.00) |
0.184 (1.00) |
0.626 (1.00) |
0.803 (1.00) |
0.571 (1.00) |
0.666 (1.00) |
0.2 (1.00) |
0.176 (1.00) |
0.346 (1.00) |
| Amp Peak 10(7p22 3) | 83 (47%) | 94 |
0.619 (1.00) |
0.00261 (1.00) |
0.0452 (1.00) |
0.464 (1.00) |
0.194 (1.00) |
0.771 (1.00) |
0.0113 (1.00) |
0.608 (1.00) |
1 (1.00) |
0.941 (1.00) |
0.428 (1.00) |
| Amp Peak 11(7p11 2) | 76 (43%) | 101 |
0.653 (1.00) |
0.00743 (1.00) |
0.0645 (1.00) |
0.31 (1.00) |
0.0697 (1.00) |
0.959 (1.00) |
0.0696 (1.00) |
0.261 (1.00) |
0.393 (1.00) |
0.777 (1.00) |
0.939 (1.00) |
| Amp Peak 12(7q21 2) | 79 (45%) | 98 |
0.977 (1.00) |
0.0185 (1.00) |
0.0306 (1.00) |
0.695 (1.00) |
0.182 (1.00) |
0.253 (1.00) |
0.0234 (1.00) |
0.271 (1.00) |
1 (1.00) |
0.872 (1.00) |
0.44 (1.00) |
| Amp Peak 13(8p23 1) | 63 (36%) | 114 |
0.686 (1.00) |
0.432 (1.00) |
0.203 (1.00) |
0.745 (1.00) |
0.447 (1.00) |
0.811 (1.00) |
0.474 (1.00) |
0.388 (1.00) |
0.0548 (1.00) |
0.16 (1.00) |
0.177 (1.00) |
| Amp Peak 14(8q24 21) | 109 (62%) | 68 |
0.885 (1.00) |
0.0107 (1.00) |
0.346 (1.00) |
0.217 (1.00) |
0.00125 (1.00) |
0.743 (1.00) |
0.46 (1.00) |
0.355 (1.00) |
1 (1.00) |
0.0918 (1.00) |
0.623 (1.00) |
| Amp Peak 15(9p24 1) | 24 (14%) | 153 |
0.748 (1.00) |
0.858 (1.00) |
0.654 (1.00) |
0.724 (1.00) |
0.212 (1.00) |
0.4 (1.00) |
1 (1.00) |
0.0632 (1.00) |
0.137 (1.00) |
0.36 (1.00) |
0.434 (1.00) |
| Amp Peak 16(9q34 3) | 41 (23%) | 136 |
0.282 (1.00) |
0.082 (1.00) |
1 (1.00) |
0.11 (1.00) |
0.194 (1.00) |
0.644 (1.00) |
0.687 (1.00) |
0.146 (1.00) |
0.0822 (1.00) |
0.788 (1.00) |
0.746 (1.00) |
| Amp Peak 17(10q26 13) | 36 (20%) | 141 |
0.357 (1.00) |
0.185 (1.00) |
0.849 (1.00) |
0.551 (1.00) |
0.722 (1.00) |
0.975 (1.00) |
0.709 (1.00) |
0.667 (1.00) |
0.269 (1.00) |
0.952 (1.00) |
0.449 (1.00) |
| Amp Peak 18(11p13) | 29 (16%) | 148 |
0.944 (1.00) |
0.518 (1.00) |
0.407 (1.00) |
0.666 (1.00) |
0.279 (1.00) |
0.272 (1.00) |
0.29 (1.00) |
0.434 (1.00) |
1 (1.00) |
0.572 (1.00) |
0.233 (1.00) |
| Amp Peak 19(11q13 3) | 33 (19%) | 144 |
0.141 (1.00) |
0.416 (1.00) |
0.0182 (1.00) |
0.527 (1.00) |
0.614 (1.00) |
0.696 (1.00) |
0.379 (1.00) |
0.487 (1.00) |
1 (1.00) |
0.679 (1.00) |
0.72 (1.00) |
| Amp Peak 20(12p12 1) | 40 (23%) | 137 |
0.919 (1.00) |
0.601 (1.00) |
0.36 (1.00) |
0.32 (1.00) |
0.0752 (1.00) |
0.0187 (1.00) |
0.527 (1.00) |
0.0136 (1.00) |
0.589 (1.00) |
0.111 (1.00) |
0.0127 (1.00) |
| Amp Peak 21(12q15) | 40 (23%) | 137 |
0.842 (1.00) |
0.839 (1.00) |
0.36 (1.00) |
0.908 (1.00) |
0.684 (1.00) |
0.072 (1.00) |
0.289 (1.00) |
0.374 (1.00) |
0.316 (1.00) |
0.336 (1.00) |
0.035 (1.00) |
| Amp Peak 22(13q12 3) | 64 (36%) | 113 |
0.345 (1.00) |
0.991 (1.00) |
0.0548 (1.00) |
0.731 (1.00) |
0.493 (1.00) |
0.0672 (1.00) |
0.288 (1.00) |
0.163 (1.00) |
1 (1.00) |
0.646 (1.00) |
0.0193 (1.00) |
| Amp Peak 23(13q22 1) | 74 (42%) | 103 |
0.819 (1.00) |
0.778 (1.00) |
0.00494 (1.00) |
0.585 (1.00) |
0.867 (1.00) |
0.885 (1.00) |
0.505 (1.00) |
0.06 (1.00) |
1 (1.00) |
0.705 (1.00) |
0.64 (1.00) |
| Amp Peak 24(15q26 1) | 44 (25%) | 133 |
0.597 (1.00) |
0.42 (1.00) |
0.155 (1.00) |
0.676 (1.00) |
0.185 (1.00) |
0.178 (1.00) |
0.264 (1.00) |
0.582 (1.00) |
0.599 (1.00) |
0.423 (1.00) |
0.0907 (1.00) |
| Amp Peak 25(17q12) | 47 (27%) | 130 |
0.916 (1.00) |
0.145 (1.00) |
0.0572 (1.00) |
0.147 (1.00) |
0.15 (1.00) |
0.307 (1.00) |
0.00269 (1.00) |
0.443 (1.00) |
0.61 (1.00) |
0.00299 (1.00) |
0.241 (1.00) |
| Amp Peak 26(18q11 2) | 50 (28%) | 127 |
0.0424 (1.00) |
0.19 (1.00) |
0.234 (1.00) |
0.216 (1.00) |
0.202 (1.00) |
0.137 (1.00) |
0.515 (1.00) |
0.411 (1.00) |
0.138 (1.00) |
0.0125 (1.00) |
0.164 (1.00) |
| Amp Peak 27(19q12) | 46 (26%) | 131 |
0.18 (1.00) |
0.0774 (1.00) |
0.728 (1.00) |
0.0631 (1.00) |
0.0625 (1.00) |
0.0776 (1.00) |
0.39 (1.00) |
0.552 (1.00) |
0.0166 (1.00) |
0.0816 (1.00) |
0.0139 (1.00) |
| Amp Peak 28(20q13 2) | 108 (61%) | 69 |
0.409 (1.00) |
0.194 (1.00) |
0.000929 (0.763) |
0.0993 (1.00) |
0.00163 (1.00) |
0.593 (1.00) |
0.444 (1.00) |
0.833 (1.00) |
1 (1.00) |
0.875 (1.00) |
0.0768 (1.00) |
| Amp Peak 29(Xq26 2) | 33 (19%) | 144 |
0.717 (1.00) |
0.103 (1.00) |
0.844 (1.00) |
0.506 (1.00) |
0.943 (1.00) |
0.613 (1.00) |
0.645 (1.00) |
0.642 (1.00) |
0.585 (1.00) |
0.895 (1.00) |
0.708 (1.00) |
| Del Peak 1(1p36 11) | 43 (24%) | 134 |
0.882 (1.00) |
0.667 (1.00) |
0.37 (1.00) |
0.368 (1.00) |
0.0808 (1.00) |
0.96 (1.00) |
0.94 (1.00) |
0.482 (1.00) |
0.596 (1.00) |
0.0419 (1.00) |
0.665 (1.00) |
| Del Peak 2(1p13 2) | 31 (18%) | 146 |
0.338 (1.00) |
0.486 (1.00) |
0.689 (1.00) |
0.4 (1.00) |
0.673 (1.00) |
0.884 (1.00) |
0.581 (1.00) |
0.773 (1.00) |
1 (1.00) |
0.4 (1.00) |
0.286 (1.00) |
| Del Peak 3(1q44) | 12 (7%) | 165 |
0.0181 (1.00) |
0.0389 (1.00) |
0.766 (1.00) |
0.79 (1.00) |
0.122 (1.00) |
0.522 (1.00) |
0.494 (1.00) |
0.752 (1.00) |
1 (1.00) |
0.166 (1.00) |
0.457 (1.00) |
| Del Peak 4(2q32 1) | 20 (11%) | 157 |
0.345 (1.00) |
0.695 (1.00) |
0.809 (1.00) |
0.0466 (1.00) |
0.327 (1.00) |
0.428 (1.00) |
0.361 (1.00) |
0.333 (1.00) |
0.455 (1.00) |
0.288 (1.00) |
0.512 (1.00) |
| Del Peak 5(2q37 2) | 23 (13%) | 154 |
0.536 (1.00) |
0.0379 (1.00) |
0.493 (1.00) |
0.00367 (1.00) |
0.349 (1.00) |
0.289 (1.00) |
0.119 (1.00) |
0.347 (1.00) |
0.506 (1.00) |
0.0462 (1.00) |
0.0858 (1.00) |
| Del Peak 6(3p26 1) | 47 (27%) | 130 |
0.906 (1.00) |
0.125 (1.00) |
0.606 (1.00) |
0.748 (1.00) |
0.503 (1.00) |
0.135 (1.00) |
0.501 (1.00) |
0.605 (1.00) |
1 (1.00) |
0.346 (1.00) |
0.794 (1.00) |
| Del Peak 7(3p14 2) | 58 (33%) | 119 |
0.715 (1.00) |
0.923 (1.00) |
0.516 (1.00) |
0.238 (1.00) |
0.202 (1.00) |
0.607 (1.00) |
0.667 (1.00) |
0.319 (1.00) |
0.663 (1.00) |
0.014 (1.00) |
0.544 (1.00) |
| Del Peak 8(3q26 31) | 18 (10%) | 159 |
0.71 (1.00) |
0.968 (1.00) |
0.621 (1.00) |
0.553 (1.00) |
0.439 (1.00) |
0.409 (1.00) |
0.105 (1.00) |
0.619 (1.00) |
0.419 (1.00) |
0.719 (1.00) |
0.0969 (1.00) |
| Del Peak 9(4q22 1) | 66 (37%) | 111 |
0.496 (1.00) |
0.109 (1.00) |
0.753 (1.00) |
0.239 (1.00) |
0.0219 (1.00) |
0.175 (1.00) |
0.772 (1.00) |
0.449 (1.00) |
0.065 (1.00) |
0.228 (1.00) |
0.197 (1.00) |
| Del Peak 10(4q34 3) | 64 (36%) | 113 |
0.879 (1.00) |
0.0996 (1.00) |
0.523 (1.00) |
0.0564 (1.00) |
0.0182 (1.00) |
0.309 (1.00) |
0.768 (1.00) |
0.111 (1.00) |
0.354 (1.00) |
0.352 (1.00) |
0.82 (1.00) |
| Del Peak 11(5q11 2) | 48 (27%) | 129 |
0.6 (1.00) |
0.0532 (1.00) |
0.604 (1.00) |
0.00282 (1.00) |
0.00617 (1.00) |
0.439 (1.00) |
0.268 (1.00) |
0.564 (1.00) |
0.614 (1.00) |
0.243 (1.00) |
0.363 (1.00) |
| Del Peak 12(6p25 3) | 39 (22%) | 138 |
0.391 (1.00) |
0.711 (1.00) |
0.359 (1.00) |
0.0175 (1.00) |
0.129 (1.00) |
0.319 (1.00) |
0.349 (1.00) |
0.863 (1.00) |
1 (1.00) |
0.37 (1.00) |
0.147 (1.00) |
| Del Peak 13(6q26) | 41 (23%) | 136 |
0.38 (1.00) |
0.851 (1.00) |
0.718 (1.00) |
0.665 (1.00) |
0.538 (1.00) |
0.521 (1.00) |
0.733 (1.00) |
0.754 (1.00) |
0.328 (1.00) |
0.107 (1.00) |
0.209 (1.00) |
| Del Peak 14(7q31 1) | 21 (12%) | 156 |
0.0651 (1.00) |
0.351 (1.00) |
0.155 (1.00) |
0.232 (1.00) |
0.701 (1.00) |
0.000829 (0.682) |
0.304 (1.00) |
0.482 (1.00) |
1 (1.00) |
0.921 (1.00) |
0.741 (1.00) |
| Del Peak 15(7q36 3) | 31 (18%) | 146 |
0.238 (1.00) |
0.802 (1.00) |
0.227 (1.00) |
0.31 (1.00) |
0.15 (1.00) |
0.00291 (1.00) |
1 (1.00) |
0.0285 (1.00) |
1 (1.00) |
0.948 (1.00) |
0.0972 (1.00) |
| Del Peak 16(8p23 2) | 45 (25%) | 132 |
0.902 (1.00) |
0.0118 (1.00) |
0.218 (1.00) |
0.435 (1.00) |
0.457 (1.00) |
0.215 (1.00) |
0.943 (1.00) |
0.36 (1.00) |
1 (1.00) |
0.0483 (1.00) |
0.0691 (1.00) |
| Del Peak 17(9p23) | 70 (40%) | 107 |
0.045 (1.00) |
0.341 (1.00) |
0.876 (1.00) |
0.297 (1.00) |
0.0994 (1.00) |
0.19 (1.00) |
0.592 (1.00) |
0.0363 (1.00) |
0.385 (1.00) |
0.749 (1.00) |
0.024 (1.00) |
| Del Peak 18(9p21 3) | 66 (37%) | 111 |
0.394 (1.00) |
0.534 (1.00) |
0.529 (1.00) |
0.516 (1.00) |
0.0313 (1.00) |
0.471 (1.00) |
0.686 (1.00) |
0.838 (1.00) |
0.363 (1.00) |
0.555 (1.00) |
0.145 (1.00) |
| Del Peak 19(9q21 11) | 37 (21%) | 140 |
0.398 (1.00) |
0.561 (1.00) |
0.576 (1.00) |
0.197 (1.00) |
0.18 (1.00) |
0.809 (1.00) |
0.217 (1.00) |
0.258 (1.00) |
0.28 (1.00) |
0.837 (1.00) |
0.391 (1.00) |
| Del Peak 20(10p14) | 24 (14%) | 153 |
0.149 (1.00) |
0.424 (1.00) |
0.654 (1.00) |
0.22 (1.00) |
0.183 (1.00) |
0.508 (1.00) |
0.678 (1.00) |
0.961 (1.00) |
0.522 (1.00) |
0.372 (1.00) |
0.503 (1.00) |
| Del Peak 21(10q22 3) | 24 (14%) | 153 |
0.846 (1.00) |
0.0858 (1.00) |
0.654 (1.00) |
0.318 (1.00) |
0.00954 (1.00) |
0.438 (1.00) |
0.384 (1.00) |
0.904 (1.00) |
0.522 (1.00) |
0.77 (1.00) |
0.209 (1.00) |
| Del Peak 23(11p15 4) | 40 (23%) | 137 |
0.274 (1.00) |
0.659 (1.00) |
0.583 (1.00) |
0.00138 (1.00) |
0.0211 (1.00) |
0.413 (1.00) |
0.938 (1.00) |
0.887 (1.00) |
0.316 (1.00) |
0.11 (1.00) |
0.188 (1.00) |
| Del Peak 24(11q23 2) | 39 (22%) | 138 |
0.14 (1.00) |
0.717 (1.00) |
0.266 (1.00) |
0.226 (1.00) |
0.483 (1.00) |
0.647 (1.00) |
0.23 (1.00) |
0.949 (1.00) |
0.304 (1.00) |
0.223 (1.00) |
0.24 (1.00) |
| Del Peak 25(12p13 31) | 26 (15%) | 151 |
0.436 (1.00) |
0.186 (1.00) |
0.829 (1.00) |
0.245 (1.00) |
0.284 (1.00) |
0.816 (1.00) |
0.693 (1.00) |
0.165 (1.00) |
0.553 (1.00) |
0.0864 (1.00) |
0.616 (1.00) |
| Del Peak 26(13q14 2) | 26 (15%) | 151 |
0.48 (1.00) |
0.771 (1.00) |
0.28 (1.00) |
0.767 (1.00) |
0.385 (1.00) |
0.81 (1.00) |
0.255 (1.00) |
0.752 (1.00) |
0.157 (1.00) |
0.11 (1.00) |
0.192 (1.00) |
| Del Peak 27(14q21 1) | 41 (23%) | 136 |
0.381 (1.00) |
0.655 (1.00) |
0.363 (1.00) |
0.191 (1.00) |
0.00262 (1.00) |
0.409 (1.00) |
0.0193 (1.00) |
0.255 (1.00) |
0.328 (1.00) |
0.842 (1.00) |
0.694 (1.00) |
| Del Peak 28(14q32 33) | 46 (26%) | 131 |
0.181 (1.00) |
0.605 (1.00) |
1 (1.00) |
0.519 (1.00) |
0.169 (1.00) |
0.17 (1.00) |
0.00365 (1.00) |
0.138 (1.00) |
0.111 (1.00) |
0.173 (1.00) |
0.557 (1.00) |
| Del Peak 29(15q11 2) | 40 (23%) | 137 |
0.448 (1.00) |
0.13 (1.00) |
0.36 (1.00) |
0.00134 (1.00) |
0.0131 (1.00) |
0.144 (1.00) |
0.882 (1.00) |
0.382 (1.00) |
0.0769 (1.00) |
0.477 (1.00) |
0.333 (1.00) |
| Del Peak 30(15q15 1) | 41 (23%) | 136 |
0.445 (1.00) |
0.51 (1.00) |
0.277 (1.00) |
0.00608 (1.00) |
0.00656 (1.00) |
0.0136 (1.00) |
0.321 (1.00) |
0.0702 (1.00) |
0.0822 (1.00) |
0.212 (1.00) |
0.0893 (1.00) |
| Del Peak 31(16p13 3) | 23 (13%) | 154 |
0.682 (1.00) |
0.00747 (1.00) |
0.177 (1.00) |
0.00691 (1.00) |
0.554 (1.00) |
0.901 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.506 (1.00) |
0.0266 (1.00) |
0.671 (1.00) |
| Del Peak 32(16q23 1) | 58 (33%) | 119 |
0.123 (1.00) |
0.417 (1.00) |
0.0328 (1.00) |
0.17 (1.00) |
0.0588 (1.00) |
0.161 (1.00) |
0.102 (1.00) |
0.362 (1.00) |
0.332 (1.00) |
0.0998 (1.00) |
0.0712 (1.00) |
| Del Peak 33(17p12) | 60 (34%) | 117 |
0.0562 (1.00) |
0.605 (1.00) |
0.419 (1.00) |
0.0448 (1.00) |
0.000683 (0.563) |
0.272 (1.00) |
0.398 (1.00) |
0.405 (1.00) |
0.0457 (1.00) |
0.0793 (1.00) |
0.9 (1.00) |
| Del Peak 34(17q24 3) | 27 (15%) | 150 |
0.357 (1.00) |
0.0109 (1.00) |
0.527 (1.00) |
0.0444 (1.00) |
0.748 (1.00) |
0.0386 (1.00) |
0.842 (1.00) |
0.771 (1.00) |
1 (1.00) |
0.194 (1.00) |
0.46 (1.00) |
| Del Peak 35(18q21 2) | 69 (39%) | 108 |
0.336 (1.00) |
0.986 (1.00) |
1 (1.00) |
0.736 (1.00) |
0.00622 (1.00) |
0.0273 (1.00) |
0.398 (1.00) |
0.54 (1.00) |
1 (1.00) |
0.0344 (1.00) |
0.00225 (1.00) |
| Del Peak 36(18q23) | 64 (36%) | 113 |
0.384 (1.00) |
0.941 (1.00) |
0.873 (1.00) |
0.988 (1.00) |
0.0127 (1.00) |
0.0185 (1.00) |
0.349 (1.00) |
0.282 (1.00) |
0.0581 (1.00) |
0.0229 (1.00) |
0.0144 (1.00) |
| Del Peak 37(19p13 3) | 53 (30%) | 124 |
0.308 (1.00) |
0.361 (1.00) |
0.00767 (1.00) |
0.526 (1.00) |
0.254 (1.00) |
0.549 (1.00) |
0.333 (1.00) |
0.905 (1.00) |
0.0287 (1.00) |
0.931 (1.00) |
0.162 (1.00) |
| Del Peak 38(19q13 11) | 24 (14%) | 153 |
0.434 (1.00) |
0.171 (1.00) |
0.654 (1.00) |
0.0176 (1.00) |
0.311 (1.00) |
0.23 (1.00) |
0.751 (1.00) |
0.889 (1.00) |
0.522 (1.00) |
0.563 (1.00) |
0.342 (1.00) |
| Del Peak 39(20p12 1) | 27 (15%) | 150 |
0.0628 (1.00) |
0.726 (1.00) |
0.833 (1.00) |
0.55 (1.00) |
0.479 (1.00) |
0.729 (1.00) |
0.704 (1.00) |
0.873 (1.00) |
0.167 (1.00) |
1 (1.00) |
0.199 (1.00) |
| Del Peak 40(20p12 1) | 27 (15%) | 150 |
0.0628 (1.00) |
0.726 (1.00) |
0.833 (1.00) |
0.55 (1.00) |
0.479 (1.00) |
0.729 (1.00) |
0.704 (1.00) |
0.873 (1.00) |
0.167 (1.00) |
1 (1.00) |
0.199 (1.00) |
| Del Peak 41(21q11 2) | 54 (31%) | 123 |
0.873 (1.00) |
0.192 (1.00) |
0.619 (1.00) |
0.369 (1.00) |
0.0225 (1.00) |
0.668 (1.00) |
0.783 (1.00) |
0.984 (1.00) |
0.642 (1.00) |
0.427 (1.00) |
0.524 (1.00) |
| Del Peak 42(21q22 13) | 58 (33%) | 119 |
0.846 (1.00) |
0.296 (1.00) |
0.624 (1.00) |
0.476 (1.00) |
0.0341 (1.00) |
0.333 (1.00) |
0.917 (1.00) |
0.837 (1.00) |
1 (1.00) |
0.242 (1.00) |
0.333 (1.00) |
| Del Peak 43(22q13 31) | 53 (30%) | 124 |
0.474 (1.00) |
0.277 (1.00) |
1 (1.00) |
0.0207 (1.00) |
0.0803 (1.00) |
0.72 (1.00) |
0.415 (1.00) |
0.913 (1.00) |
0.159 (1.00) |
0.215 (1.00) |
0.406 (1.00) |
| Del Peak 44(Xp22 2) | 30 (17%) | 147 |
0.408 (1.00) |
0.721 (1.00) |
0.839 (1.00) |
0.00609 (1.00) |
0.331 (1.00) |
0.696 (1.00) |
1 (1.00) |
0.707 (1.00) |
1 (1.00) |
0.771 (1.00) |
0.881 (1.00) |
| Del Peak 45(Xp21 1) | 30 (17%) | 147 |
0.412 (1.00) |
0.357 (1.00) |
0.151 (1.00) |
0.0563 (1.00) |
0.345 (1.00) |
0.368 (1.00) |
0.794 (1.00) |
0.905 (1.00) |
0.59 (1.00) |
0.022 (1.00) |
0.115 (1.00) |
| Del Peak 46(Xq21 33) | 22 (12%) | 155 |
0.305 (1.00) |
0.629 (1.00) |
1 (1.00) |
0.379 (1.00) |
0.12 (1.00) |
0.444 (1.00) |
0.737 (1.00) |
0.157 (1.00) |
0.489 (1.00) |
0.259 (1.00) |
0.775 (1.00) |
'Del Peak 22(10q23.31) mutation analysis' versus 'PATHOLOGY.T'
P value = 0.000181 (Fisher's exact test), Q value = 0.15
Table S1. Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'
| nPatients | T1 | T2 | T3 | T4 |
|---|---|---|---|---|
| ALL | 6 | 54 | 64 | 43 |
| DEL PEAK 22(10Q23.31) MUTATED | 1 | 21 | 9 | 2 |
| DEL PEAK 22(10Q23.31) WILD-TYPE | 5 | 33 | 55 | 41 |
Figure S1. Get High-res Image Gene #51: 'Del Peak 22(10q23.31) mutation analysis' versus Clinical Feature #5: 'PATHOLOGY.T'
Methods & Data
Input
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = STAD-TP.clin.merged.picked.txt
-
Number of patients = 177
-
Number of significantly arm-level cnvs = 75
-
Number of selected clinical features = 11
-
Exclude genes that fewer than K tumors have mutations, K = 3
Survival analysis
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
Student's t-test analysis
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
Fisher's exact test
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
Chi-square test
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
Q value calculation
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.
Download Results
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.
References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2013
Broad Institute TCGA GDAC as part of the TCGA Research Network.
All rights reserved.