This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between subtypes identified by 63 different clustering approaches and 12 clinical features across 125 patients, one significant finding detected with Q value < 0.25.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 1(1p34.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 2(1q21.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 3(1q23.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 4(3p25.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 5(3q26.32) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 6(4p16.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 7(4q13.3) mutation analysis'. These subtypes correlate to 'KARNOFSKY.PERFORMANCE.SCORE'.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 8(5p15.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 9(6p22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 10(6q12) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 11(6q21) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 12(7p11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 13(8p11.23) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 14(8p11.21) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 15(8q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 16(8q24.21) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 17(10p15.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 18(11q13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 19(12q15) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 20(13q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 21(16p12.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 22(17q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 23(17q12) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 24(19q12) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 25(19q13.43) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 26(20q11.21) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 27(22q11.23) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Del Peak 1(1p36.11) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 2(1q32.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 3(2q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 4(2q34) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 5(2q37.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 6(3p21.31) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 7(3p14.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 8(3p12.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 9(4q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 10(4q34.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 11(5q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 12(5q35.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 13(6p25.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 14(6q21) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 15(6q27) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 16(8p23.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 17(8p21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 18(9p23) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 19(9p21.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 20(10p12.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 21(10q23.31) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 22(11p15.5) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 23(11q25) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Del Peak 24(13q14.2) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Del Peak 25(14q12) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Del Peak 26(14q32.31) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 27(15q13.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 28(16p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 29(16q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 30(17p12) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 31(18q23) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 32(19p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Del Peak 33(22q13.32) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Del Peak 34(Xp11.3) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Del Peak 35(Xq21.33) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Del Peak 36(Xq22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
NUMBERPACKYEARSSMOKED | STOPPEDSMOKINGYEAR | TOBACCOSMOKINGHISTORYINDICATOR |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
Statistical Tests | logrank test | t-test | Fisher's exact test | t-test | t-test | t-test | t-test | Fisher's exact test | Chi-square test | t-test | t-test | Fisher's exact test |
Amp Peak 1(1p34 2) |
0.448 (1.00) |
0.402 (1.00) |
0.271 (1.00) |
0.193 (1.00) |
0.548 (1.00) |
0.814 (1.00) |
0.73 (1.00) |
0.639 (1.00) |
0.414 (1.00) |
0.425 (1.00) |
0.221 (1.00) |
|
Amp Peak 2(1q21 3) |
0.266 (1.00) |
0.52 (1.00) |
0.841 (1.00) |
0.366 (1.00) |
0.118 (1.00) |
0.266 (1.00) |
0.276 (1.00) |
0.319 (1.00) |
0.0241 (1.00) |
0.0804 (1.00) |
0.0572 (1.00) |
|
Amp Peak 3(1q23 3) |
0.849 (1.00) |
0.532 (1.00) |
0.545 (1.00) |
0.301 (1.00) |
0.478 (1.00) |
0.464 (1.00) |
0.396 (1.00) |
0.0274 (1.00) |
0.0959 (1.00) |
0.0708 (1.00) |
0.0888 (1.00) |
|
Amp Peak 4(3p25 2) |
0.095 (1.00) |
0.563 (1.00) |
0.0673 (1.00) |
0.263 (1.00) |
0.363 (1.00) |
0.275 (1.00) |
0.526 (1.00) |
0.777 (1.00) |
0.808 (1.00) |
0.444 (1.00) |
0.294 (1.00) |
|
Amp Peak 5(3q26 32) |
0.0171 (1.00) |
0.853 (1.00) |
0.682 (1.00) |
0.751 (1.00) |
0.932 (1.00) |
0.342 (1.00) |
0.831 (1.00) |
0.759 (1.00) |
0.209 (1.00) |
0.969 (1.00) |
0.541 (1.00) |
|
Amp Peak 6(4p16 3) |
0.0371 (1.00) |
0.675 (1.00) |
0.0783 (1.00) |
0.391 (1.00) |
0.728 (1.00) |
0.391 (1.00) |
0.561 (1.00) |
0.00522 (1.00) |
0.171 (1.00) |
0.972 (1.00) |
0.061 (1.00) |
|
Amp Peak 7(4q13 3) |
0.462 (1.00) |
0.092 (1.00) |
0.0712 (1.00) |
7.05e-05 (0.0489) |
0.742 (1.00) |
0.674 (1.00) |
0.885 (1.00) |
0.794 (1.00) |
0.798 (1.00) |
0.879 (1.00) |
0.666 (1.00) |
|
Amp Peak 8(5p15 1) |
0.787 (1.00) |
0.504 (1.00) |
0.311 (1.00) |
0.595 (1.00) |
0.615 (1.00) |
0.353 (1.00) |
0.119 (1.00) |
0.339 (1.00) |
0.00137 (0.945) |
0.0995 (1.00) |
0.828 (1.00) |
|
Amp Peak 9(6p22 3) |
0.477 (1.00) |
0.525 (1.00) |
0.412 (1.00) |
0.703 (1.00) |
0.985 (1.00) |
0.294 (1.00) |
0.127 (1.00) |
1 (1.00) |
0.257 (1.00) |
0.0131 (1.00) |
0.441 (1.00) |
|
Amp Peak 10(6q12) |
0.354 (1.00) |
0.0805 (1.00) |
0.185 (1.00) |
0.256 (1.00) |
0.183 (1.00) |
0.395 (1.00) |
0.162 (1.00) |
1 (1.00) |
0.904 (1.00) |
0.0762 (1.00) |
0.626 (1.00) |
|
Amp Peak 11(6q21) |
0.967 (1.00) |
0.582 (1.00) |
0.743 (1.00) |
0.364 (1.00) |
0.201 (1.00) |
0.482 (1.00) |
0.39 (1.00) |
0.702 (1.00) |
0.59 (1.00) |
0.873 (1.00) |
1 (1.00) |
|
Amp Peak 12(7p11 2) |
0.552 (1.00) |
0.0553 (1.00) |
0.689 (1.00) |
0.524 (1.00) |
0.706 (1.00) |
0.557 (1.00) |
0.0577 (1.00) |
0.631 (1.00) |
0.132 (1.00) |
0.999 (1.00) |
0.64 (1.00) |
|
Amp Peak 13(8p11 23) |
0.328 (1.00) |
0.86 (1.00) |
0.395 (1.00) |
0.943 (1.00) |
0.103 (1.00) |
0.00534 (1.00) |
0.265 (1.00) |
0.505 (1.00) |
0.872 (1.00) |
0.912 (1.00) |
0.677 (1.00) |
|
Amp Peak 14(8p11 21) |
0.00967 (1.00) |
0.459 (1.00) |
0.131 (1.00) |
0.578 (1.00) |
0.163 (1.00) |
0.000881 (0.609) |
0.096 (1.00) |
0.232 (1.00) |
0.862 (1.00) |
0.642 (1.00) |
0.936 (1.00) |
|
Amp Peak 15(8q22 3) |
0.241 (1.00) |
0.968 (1.00) |
0.0402 (1.00) |
0.398 (1.00) |
0.197 (1.00) |
0.828 (1.00) |
0.308 (1.00) |
0.708 (1.00) |
0.153 (1.00) |
0.115 (1.00) |
1 (1.00) |
|
Amp Peak 16(8q24 21) |
0.0912 (1.00) |
0.691 (1.00) |
0.0623 (1.00) |
0.41 (1.00) |
0.485 (1.00) |
0.995 (1.00) |
0.629 (1.00) |
0.585 (1.00) |
0.467 (1.00) |
0.149 (1.00) |
0.846 (1.00) |
|
Amp Peak 17(10p15 1) |
0.714 (1.00) |
0.0618 (1.00) |
1 (1.00) |
0.687 (1.00) |
0.972 (1.00) |
0.243 (1.00) |
0.546 (1.00) |
0.876 (1.00) |
0.108 (1.00) |
0.553 (1.00) |
0.638 (1.00) |
|
Amp Peak 18(11q13 3) |
0.853 (1.00) |
0.32 (1.00) |
0.535 (1.00) |
0.752 (1.00) |
0.86 (1.00) |
0.695 (1.00) |
0.0248 (1.00) |
0.26 (1.00) |
0.0898 (1.00) |
0.334 (1.00) |
0.555 (1.00) |
|
Amp Peak 19(12q15) |
0.416 (1.00) |
0.811 (1.00) |
0.83 (1.00) |
0.592 (1.00) |
0.167 (1.00) |
0.427 (1.00) |
0.393 (1.00) |
0.388 (1.00) |
0.217 (1.00) |
0.546 (1.00) |
0.237 (1.00) |
|
Amp Peak 20(13q22 1) |
0.397 (1.00) |
0.129 (1.00) |
0.835 (1.00) |
0.862 (1.00) |
0.0647 (1.00) |
0.406 (1.00) |
0.816 (1.00) |
0.899 (1.00) |
0.831 (1.00) |
0.573 (1.00) |
0.496 (1.00) |
|
Amp Peak 21(16p12 1) |
0.753 (1.00) |
0.882 (1.00) |
1 (1.00) |
0.375 (1.00) |
0.862 (1.00) |
0.378 (1.00) |
0.661 (1.00) |
0.582 (1.00) |
0.296 (1.00) |
0.911 (1.00) |
0.416 (1.00) |
|
Amp Peak 22(17q11 2) |
0.824 (1.00) |
0.365 (1.00) |
1 (1.00) |
0.0164 (1.00) |
0.784 (1.00) |
0.105 (1.00) |
0.721 (1.00) |
0.241 (1.00) |
0.103 (1.00) |
0.697 (1.00) |
0.0559 (1.00) |
|
Amp Peak 23(17q12) |
0.345 (1.00) |
0.403 (1.00) |
1 (1.00) |
0.0578 (1.00) |
0.3 (1.00) |
0.459 (1.00) |
0.298 (1.00) |
0.294 (1.00) |
0.277 (1.00) |
0.767 (1.00) |
0.135 (1.00) |
|
Amp Peak 24(19q12) |
0.262 (1.00) |
0.274 (1.00) |
1 (1.00) |
0.498 (1.00) |
0.561 (1.00) |
0.0854 (1.00) |
0.19 (1.00) |
0.661 (1.00) |
0.323 (1.00) |
0.143 (1.00) |
0.256 (1.00) |
|
Amp Peak 25(19q13 43) |
0.186 (1.00) |
0.323 (1.00) |
0.682 (1.00) |
0.479 (1.00) |
0.785 (1.00) |
0.165 (1.00) |
0.431 (1.00) |
0.22 (1.00) |
0.0923 (1.00) |
0.0615 (1.00) |
0.091 (1.00) |
|
Amp Peak 26(20q11 21) |
0.931 (1.00) |
0.427 (1.00) |
1 (1.00) |
0.61 (1.00) |
0.0293 (1.00) |
0.172 (1.00) |
0.654 (1.00) |
1 (1.00) |
0.661 (1.00) |
0.589 (1.00) |
0.675 (1.00) |
|
Amp Peak 27(22q11 23) |
0.0754 (1.00) |
0.458 (1.00) |
0.162 (1.00) |
0.684 (1.00) |
0.507 (1.00) |
0.879 (1.00) |
0.114 (1.00) |
0.842 (1.00) |
0.835 (1.00) |
0.718 (1.00) |
0.426 (1.00) |
|
Del Peak 1(1p36 11) |
0.18 (1.00) |
0.115 (1.00) |
1 (1.00) |
0.942 (1.00) |
0.544 (1.00) |
0.348 (1.00) |
0.355 (1.00) |
0.697 (1.00) |
0.00856 (1.00) |
0.36 (1.00) |
0.598 (1.00) |
|
Del Peak 2(1q32 1) |
0.69 (1.00) |
0.135 (1.00) |
0.0369 (1.00) |
0.666 (1.00) |
0.00901 (1.00) |
0.0715 (1.00) |
0.683 (1.00) |
0.864 (1.00) |
0.431 (1.00) |
0.32 (1.00) |
0.332 (1.00) |
|
Del Peak 3(2q22 1) |
0.301 (1.00) |
0.815 (1.00) |
0.121 (1.00) |
0.534 (1.00) |
0.944 (1.00) |
0.602 (1.00) |
0.246 (1.00) |
0.213 (1.00) |
0.868 (1.00) |
0.713 (1.00) |
0.458 (1.00) |
|
Del Peak 4(2q34) |
0.323 (1.00) |
0.246 (1.00) |
0.684 (1.00) |
0.632 (1.00) |
0.424 (1.00) |
0.819 (1.00) |
0.263 (1.00) |
0.679 (1.00) |
0.834 (1.00) |
0.41 (1.00) |
0.514 (1.00) |
|
Del Peak 5(2q37 1) |
0.545 (1.00) |
0.42 (1.00) |
0.0434 (1.00) |
0.433 (1.00) |
0.17 (1.00) |
0.589 (1.00) |
0.322 (1.00) |
0.445 (1.00) |
0.587 (1.00) |
0.944 (1.00) |
0.312 (1.00) |
|
Del Peak 6(3p21 31) |
0.966 (1.00) |
0.904 (1.00) |
0.524 (1.00) |
0.63 (1.00) |
0.373 (1.00) |
0.203 (1.00) |
0.0264 (1.00) |
0.584 (1.00) |
0.802 (1.00) |
0.206 (1.00) |
0.749 (1.00) |
|
Del Peak 7(3p14 2) |
0.398 (1.00) |
0.477 (1.00) |
0.668 (1.00) |
0.63 (1.00) |
0.815 (1.00) |
0.508 (1.00) |
0.0492 (1.00) |
0.664 (1.00) |
0.449 (1.00) |
0.0722 (1.00) |
0.7 (1.00) |
|
Del Peak 8(3p12 3) |
0.619 (1.00) |
0.118 (1.00) |
0.509 (1.00) |
0.105 (1.00) |
0.817 (1.00) |
0.954 (1.00) |
0.114 (1.00) |
0.487 (1.00) |
0.449 (1.00) |
0.184 (1.00) |
0.817 (1.00) |
|
Del Peak 9(4q22 1) |
0.891 (1.00) |
0.0966 (1.00) |
0.219 (1.00) |
0.861 (1.00) |
0.912 (1.00) |
0.359 (1.00) |
0.103 (1.00) |
0.0826 (1.00) |
0.928 (1.00) |
0.209 (1.00) |
0.839 (1.00) |
|
Del Peak 10(4q34 2) |
0.318 (1.00) |
0.112 (1.00) |
1 (1.00) |
0.631 (1.00) |
0.211 (1.00) |
0.059 (1.00) |
0.884 (1.00) |
1 (1.00) |
0.637 (1.00) |
0.463 (1.00) |
0.112 (1.00) |
|
Del Peak 11(5q11 2) |
0.914 (1.00) |
0.00649 (1.00) |
0.311 (1.00) |
0.549 (1.00) |
0.152 (1.00) |
0.883 (1.00) |
0.323 (1.00) |
0.379 (1.00) |
0.134 (1.00) |
0.279 (1.00) |
0.00201 (1.00) |
|
Del Peak 12(5q35 1) |
0.678 (1.00) |
0.0492 (1.00) |
0.104 (1.00) |
0.414 (1.00) |
0.797 (1.00) |
0.773 (1.00) |
0.235 (1.00) |
0.0703 (1.00) |
0.314 (1.00) |
0.185 (1.00) |
0.00204 (1.00) |
|
Del Peak 13(6p25 3) |
0.303 (1.00) |
0.83 (1.00) |
0.178 (1.00) |
0.154 (1.00) |
0.532 (1.00) |
0.611 (1.00) |
0.158 (1.00) |
0.258 (1.00) |
0.0153 (1.00) |
0.0442 (1.00) |
0.045 (1.00) |
|
Del Peak 14(6q21) |
0.165 (1.00) |
0.177 (1.00) |
1 (1.00) |
0.966 (1.00) |
0.535 (1.00) |
0.797 (1.00) |
0.532 (1.00) |
0.758 (1.00) |
0.0166 (1.00) |
0.00385 (1.00) |
0.000486 (0.336) |
|
Del Peak 15(6q27) |
0.081 (1.00) |
0.46 (1.00) |
0.538 (1.00) |
0.364 (1.00) |
0.862 (1.00) |
0.999 (1.00) |
0.0955 (1.00) |
0.574 (1.00) |
0.0256 (1.00) |
0.00684 (1.00) |
0.00649 (1.00) |
|
Del Peak 16(8p23 3) |
0.942 (1.00) |
0.594 (1.00) |
0.421 (1.00) |
0.906 (1.00) |
0.842 (1.00) |
0.208 (1.00) |
0.682 (1.00) |
0.0978 (1.00) |
0.176 (1.00) |
0.666 (1.00) |
0.106 (1.00) |
|
Del Peak 17(8p21 1) |
0.895 (1.00) |
0.328 (1.00) |
0.223 (1.00) |
0.729 (1.00) |
0.877 (1.00) |
0.435 (1.00) |
0.255 (1.00) |
0.0266 (1.00) |
0.178 (1.00) |
0.33 (1.00) |
0.0285 (1.00) |
|
Del Peak 18(9p23) |
0.516 (1.00) |
0.831 (1.00) |
0.424 (1.00) |
0.753 (1.00) |
0.994 (1.00) |
0.23 (1.00) |
0.36 (1.00) |
0.873 (1.00) |
0.446 (1.00) |
0.539 (1.00) |
0.834 (1.00) |
|
Del Peak 19(9p21 3) |
0.378 (1.00) |
0.798 (1.00) |
0.412 (1.00) |
0.975 (1.00) |
0.133 (1.00) |
0.265 (1.00) |
0.521 (1.00) |
1 (1.00) |
0.0604 (1.00) |
0.517 (1.00) |
0.731 (1.00) |
|
Del Peak 20(10p12 1) |
0.81 (1.00) |
0.321 (1.00) |
0.798 (1.00) |
0.635 (1.00) |
0.286 (1.00) |
0.659 (1.00) |
0.0284 (1.00) |
0.676 (1.00) |
0.603 (1.00) |
0.303 (1.00) |
0.722 (1.00) |
|
Del Peak 21(10q23 31) |
0.713 (1.00) |
0.00698 (1.00) |
1 (1.00) |
0.0916 (1.00) |
0.949 (1.00) |
0.48 (1.00) |
0.258 (1.00) |
0.735 (1.00) |
0.0439 (1.00) |
0.196 (1.00) |
0.0585 (1.00) |
|
Del Peak 22(11p15 5) |
0.455 (1.00) |
0.00652 (1.00) |
1 (1.00) |
0.00871 (1.00) |
0.92 (1.00) |
0.0577 (1.00) |
0.226 (1.00) |
0.329 (1.00) |
0.223 (1.00) |
0.194 (1.00) |
0.0856 (1.00) |
|
Del Peak 23(11q25) |
0.648 (1.00) |
0.451 (1.00) |
1 (1.00) |
0.966 (1.00) |
0.376 (1.00) |
0.674 (1.00) |
0.1 (1.00) |
0.634 (1.00) |
0.224 (1.00) |
0.0426 (1.00) |
0.291 (1.00) |
|
Del Peak 24(13q14 2) |
0.294 (1.00) |
0.0891 (1.00) |
0.302 (1.00) |
0.753 (1.00) |
0.577 (1.00) |
0.588 (1.00) |
0.0302 (1.00) |
1 (1.00) |
0.152 (1.00) |
0.226 (1.00) |
0.0606 (1.00) |
|
Del Peak 25(14q12) |
0.347 (1.00) |
0.311 (1.00) |
0.178 (1.00) |
0.487 (1.00) |
0.0477 (1.00) |
0.607 (1.00) |
0.616 (1.00) |
1 (1.00) |
0.153 (1.00) |
0.175 (1.00) |
0.0755 (1.00) |
|
Del Peak 26(14q32 31) |
0.735 (1.00) |
0.187 (1.00) |
0.0709 (1.00) |
0.312 (1.00) |
0.142 (1.00) |
0.319 (1.00) |
0.306 (1.00) |
0.499 (1.00) |
0.981 (1.00) |
0.65 (1.00) |
0.599 (1.00) |
|
Del Peak 27(15q13 1) |
0.344 (1.00) |
0.201 (1.00) |
0.532 (1.00) |
0.285 (1.00) |
0.209 (1.00) |
0.302 (1.00) |
0.0165 (1.00) |
0.0862 (1.00) |
0.198 (1.00) |
0.502 (1.00) |
0.174 (1.00) |
|
Del Peak 28(16p13 3) |
0.236 (1.00) |
0.432 (1.00) |
0.835 (1.00) |
0.862 (1.00) |
0.394 (1.00) |
0.757 (1.00) |
0.206 (1.00) |
0.86 (1.00) |
0.584 (1.00) |
0.812 (1.00) |
0.47 (1.00) |
|
Del Peak 29(16q23 1) |
0.42 (1.00) |
0.823 (1.00) |
0.82 (1.00) |
0.127 (1.00) |
0.808 (1.00) |
0.304 (1.00) |
0.00435 (1.00) |
0.735 (1.00) |
0.0275 (1.00) |
0.172 (1.00) |
0.194 (1.00) |
|
Del Peak 30(17p12) |
0.0699 (1.00) |
0.43 (1.00) |
0.543 (1.00) |
0.827 (1.00) |
0.865 (1.00) |
0.66 (1.00) |
0.801 (1.00) |
0.801 (1.00) |
0.315 (1.00) |
0.542 (1.00) |
0.0168 (1.00) |
|
Del Peak 31(18q23) |
0.126 (1.00) |
0.0675 (1.00) |
0.839 (1.00) |
0.125 (1.00) |
0.121 (1.00) |
0.201 (1.00) |
0.661 (1.00) |
0.75 (1.00) |
0.944 (1.00) |
0.445 (1.00) |
0.713 (1.00) |
|
Del Peak 32(19p13 3) |
0.776 (1.00) |
0.399 (1.00) |
0.677 (1.00) |
0.517 (1.00) |
0.337 (1.00) |
0.3 (1.00) |
0.663 (1.00) |
0.0429 (1.00) |
0.153 (1.00) |
0.611 (1.00) |
0.132 (1.00) |
|
Del Peak 33(22q13 32) |
0.658 (1.00) |
0.498 (1.00) |
0.677 (1.00) |
0.0926 (1.00) |
0.669 (1.00) |
0.262 (1.00) |
0.108 (1.00) |
0.0189 (1.00) |
0.776 (1.00) |
0.394 (1.00) |
0.307 (1.00) |
|
Del Peak 34(Xp11 3) |
0.973 (1.00) |
0.233 (1.00) |
0.37 (1.00) |
0.607 (1.00) |
0.26 (1.00) |
0.543 (1.00) |
0.368 (1.00) |
0.901 (1.00) |
0.223 (1.00) |
0.931 (1.00) |
0.537 (1.00) |
|
Del Peak 35(Xq21 33) |
0.495 (1.00) |
0.928 (1.00) |
1 (1.00) |
0.508 (1.00) |
0.763 (1.00) |
0.296 (1.00) |
0.0474 (1.00) |
0.475 (1.00) |
0.293 (1.00) |
0.958 (1.00) |
0.702 (1.00) |
|
Del Peak 36(Xq22 3) |
0.0998 (1.00) |
0.806 (1.00) |
0.809 (1.00) |
0.683 (1.00) |
0.894 (1.00) |
0.294 (1.00) |
0.213 (1.00) |
0.467 (1.00) |
0.475 (1.00) |
0.993 (1.00) |
0.937 (1.00) |
Cluster Labels | AMP PEAK 1(1P34.2) MUTATED | AMP PEAK 1(1P34.2) WILD-TYPE |
---|---|---|
Number of samples | 36 | 89 |
Cluster Labels | AMP PEAK 2(1Q21.3) MUTATED | AMP PEAK 2(1Q21.3) WILD-TYPE |
---|---|---|
Number of samples | 63 | 62 |
Cluster Labels | AMP PEAK 3(1Q23.3) MUTATED | AMP PEAK 3(1Q23.3) WILD-TYPE |
---|---|---|
Number of samples | 67 | 58 |
Cluster Labels | AMP PEAK 4(3P25.2) MUTATED | AMP PEAK 4(3P25.2) WILD-TYPE |
---|---|---|
Number of samples | 60 | 65 |
Cluster Labels | AMP PEAK 5(3Q26.32) MUTATED | AMP PEAK 5(3Q26.32) WILD-TYPE |
---|---|---|
Number of samples | 73 | 52 |
Cluster Labels | AMP PEAK 6(4P16.3) MUTATED | AMP PEAK 6(4P16.3) WILD-TYPE |
---|---|---|
Number of samples | 26 | 99 |
Cluster Labels | AMP PEAK 7(4Q13.3) MUTATED | AMP PEAK 7(4Q13.3) WILD-TYPE |
---|---|---|
Number of samples | 17 | 108 |
P value = 7.05e-05 (t-test), Q value = 0.049
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 37 | 78.1 (16.3) |
AMP PEAK 7(4Q13.3) MUTATED | 3 | 90.0 (0.0) |
AMP PEAK 7(4Q13.3) WILD-TYPE | 34 | 77.1 (16.6) |
Cluster Labels | AMP PEAK 8(5P15.1) MUTATED | AMP PEAK 8(5P15.1) WILD-TYPE |
---|---|---|
Number of samples | 60 | 65 |
Cluster Labels | AMP PEAK 9(6P22.3) MUTATED | AMP PEAK 9(6P22.3) WILD-TYPE |
---|---|---|
Number of samples | 49 | 76 |
Cluster Labels | AMP PEAK 10(6Q12) MUTATED | AMP PEAK 10(6Q12) WILD-TYPE |
---|---|---|
Number of samples | 22 | 103 |
Cluster Labels | AMP PEAK 11(6Q21) MUTATED | AMP PEAK 11(6Q21) WILD-TYPE |
---|---|---|
Number of samples | 13 | 112 |
Cluster Labels | AMP PEAK 12(7P11.2) MUTATED | AMP PEAK 12(7P11.2) WILD-TYPE |
---|---|---|
Number of samples | 64 | 61 |
Cluster Labels | AMP PEAK 13(8P11.23) MUTATED | AMP PEAK 13(8P11.23) WILD-TYPE |
---|---|---|
Number of samples | 43 | 82 |
Cluster Labels | AMP PEAK 14(8P11.21) MUTATED | AMP PEAK 14(8P11.21) WILD-TYPE |
---|---|---|
Number of samples | 41 | 84 |
Cluster Labels | AMP PEAK 15(8Q22.3) MUTATED | AMP PEAK 15(8Q22.3) WILD-TYPE |
---|---|---|
Number of samples | 76 | 49 |
Cluster Labels | AMP PEAK 16(8Q24.21) MUTATED | AMP PEAK 16(8Q24.21) WILD-TYPE |
---|---|---|
Number of samples | 75 | 50 |
Cluster Labels | AMP PEAK 17(10P15.1) MUTATED | AMP PEAK 17(10P15.1) WILD-TYPE |
---|---|---|
Number of samples | 53 | 72 |
Cluster Labels | AMP PEAK 18(11Q13.3) MUTATED | AMP PEAK 18(11Q13.3) WILD-TYPE |
---|---|---|
Number of samples | 47 | 78 |
Cluster Labels | AMP PEAK 19(12Q15) MUTATED | AMP PEAK 19(12Q15) WILD-TYPE |
---|---|---|
Number of samples | 41 | 84 |
Cluster Labels | AMP PEAK 20(13Q22.1) MUTATED | AMP PEAK 20(13Q22.1) WILD-TYPE |
---|---|---|
Number of samples | 44 | 81 |
Cluster Labels | AMP PEAK 21(16P12.1) MUTATED | AMP PEAK 21(16P12.1) WILD-TYPE |
---|---|---|
Number of samples | 34 | 91 |
Cluster Labels | AMP PEAK 22(17Q11.2) MUTATED | AMP PEAK 22(17Q11.2) WILD-TYPE |
---|---|---|
Number of samples | 58 | 67 |
Cluster Labels | AMP PEAK 23(17Q12) MUTATED | AMP PEAK 23(17Q12) WILD-TYPE |
---|---|---|
Number of samples | 53 | 72 |
Cluster Labels | AMP PEAK 24(19Q12) MUTATED | AMP PEAK 24(19Q12) WILD-TYPE |
---|---|---|
Number of samples | 52 | 73 |
Cluster Labels | AMP PEAK 25(19Q13.43) MUTATED | AMP PEAK 25(19Q13.43) WILD-TYPE |
---|---|---|
Number of samples | 52 | 73 |
Cluster Labels | AMP PEAK 26(20Q11.21) MUTATED | AMP PEAK 26(20Q11.21) WILD-TYPE |
---|---|---|
Number of samples | 87 | 38 |
Cluster Labels | AMP PEAK 27(22Q11.23) MUTATED | AMP PEAK 27(22Q11.23) WILD-TYPE |
---|---|---|
Number of samples | 32 | 93 |
Cluster Labels | DEL PEAK 1(1P36.11) MUTATED | DEL PEAK 1(1P36.11) WILD-TYPE |
---|---|---|
Number of samples | 23 | 102 |
Cluster Labels | DEL PEAK 2(1Q32.1) MUTATED | DEL PEAK 2(1Q32.1) WILD-TYPE |
---|---|---|
Number of samples | 24 | 101 |
Cluster Labels | DEL PEAK 3(2Q22.1) MUTATED | DEL PEAK 3(2Q22.1) WILD-TYPE |
---|---|---|
Number of samples | 38 | 87 |
Cluster Labels | DEL PEAK 4(2Q34) MUTATED | DEL PEAK 4(2Q34) WILD-TYPE |
---|---|---|
Number of samples | 54 | 71 |
Cluster Labels | DEL PEAK 5(2Q37.1) MUTATED | DEL PEAK 5(2Q37.1) WILD-TYPE |
---|---|---|
Number of samples | 65 | 60 |
Cluster Labels | DEL PEAK 6(3P21.31) MUTATED | DEL PEAK 6(3P21.31) WILD-TYPE |
---|---|---|
Number of samples | 40 | 85 |
Cluster Labels | DEL PEAK 7(3P14.2) MUTATED | DEL PEAK 7(3P14.2) WILD-TYPE |
---|---|---|
Number of samples | 41 | 84 |
Cluster Labels | DEL PEAK 8(3P12.3) MUTATED | DEL PEAK 8(3P12.3) WILD-TYPE |
---|---|---|
Number of samples | 36 | 89 |
Cluster Labels | DEL PEAK 9(4Q22.1) MUTATED | DEL PEAK 9(4Q22.1) WILD-TYPE |
---|---|---|
Number of samples | 49 | 76 |
Cluster Labels | DEL PEAK 10(4Q34.2) MUTATED | DEL PEAK 10(4Q34.2) WILD-TYPE |
---|---|---|
Number of samples | 55 | 70 |
Cluster Labels | DEL PEAK 11(5Q11.2) MUTATED | DEL PEAK 11(5Q11.2) WILD-TYPE |
---|---|---|
Number of samples | 64 | 61 |
Cluster Labels | DEL PEAK 12(5Q35.1) MUTATED | DEL PEAK 12(5Q35.1) WILD-TYPE |
---|---|---|
Number of samples | 62 | 63 |
Cluster Labels | DEL PEAK 13(6P25.3) MUTATED | DEL PEAK 13(6P25.3) WILD-TYPE |
---|---|---|
Number of samples | 34 | 91 |
Cluster Labels | DEL PEAK 14(6Q21) MUTATED | DEL PEAK 14(6Q21) WILD-TYPE |
---|---|---|
Number of samples | 51 | 74 |
Cluster Labels | DEL PEAK 15(6Q27) MUTATED | DEL PEAK 15(6Q27) WILD-TYPE |
---|---|---|
Number of samples | 53 | 72 |
Cluster Labels | DEL PEAK 16(8P23.3) MUTATED | DEL PEAK 16(8P23.3) WILD-TYPE |
---|---|---|
Number of samples | 65 | 60 |
Cluster Labels | DEL PEAK 17(8P21.1) MUTATED | DEL PEAK 17(8P21.1) WILD-TYPE |
---|---|---|
Number of samples | 69 | 56 |
Cluster Labels | DEL PEAK 18(9P23) MUTATED | DEL PEAK 18(9P23) WILD-TYPE |
---|---|---|
Number of samples | 57 | 68 |
Cluster Labels | DEL PEAK 19(9P21.3) MUTATED | DEL PEAK 19(9P21.3) WILD-TYPE |
---|---|---|
Number of samples | 73 | 52 |
Cluster Labels | DEL PEAK 20(10P12.1) MUTATED | DEL PEAK 20(10P12.1) WILD-TYPE |
---|---|---|
Number of samples | 24 | 101 |
Cluster Labels | DEL PEAK 21(10Q23.31) MUTATED | DEL PEAK 21(10Q23.31) WILD-TYPE |
---|---|---|
Number of samples | 53 | 72 |
Cluster Labels | DEL PEAK 22(11P15.5) MUTATED | DEL PEAK 22(11P15.5) WILD-TYPE |
---|---|---|
Number of samples | 62 | 63 |
Cluster Labels | DEL PEAK 23(11Q25) MUTATED | DEL PEAK 23(11Q25) WILD-TYPE |
---|---|---|
Number of samples | 39 | 86 |
Cluster Labels | DEL PEAK 24(13Q14.2) MUTATED | DEL PEAK 24(13Q14.2) WILD-TYPE |
---|---|---|
Number of samples | 48 | 77 |
Cluster Labels | DEL PEAK 25(14Q12) MUTATED | DEL PEAK 25(14Q12) WILD-TYPE |
---|---|---|
Number of samples | 35 | 90 |
Cluster Labels | DEL PEAK 26(14Q32.31) MUTATED | DEL PEAK 26(14Q32.31) WILD-TYPE |
---|---|---|
Number of samples | 35 | 90 |
Cluster Labels | DEL PEAK 27(15Q13.1) MUTATED | DEL PEAK 27(15Q13.1) WILD-TYPE |
---|---|---|
Number of samples | 44 | 81 |
Cluster Labels | DEL PEAK 28(16P13.3) MUTATED | DEL PEAK 28(16P13.3) WILD-TYPE |
---|---|---|
Number of samples | 44 | 81 |
Cluster Labels | DEL PEAK 29(16Q23.1) MUTATED | DEL PEAK 29(16Q23.1) WILD-TYPE |
---|---|---|
Number of samples | 34 | 91 |
Cluster Labels | DEL PEAK 30(17P12) MUTATED | DEL PEAK 30(17P12) WILD-TYPE |
---|---|---|
Number of samples | 64 | 61 |
Cluster Labels | DEL PEAK 31(18Q23) MUTATED | DEL PEAK 31(18Q23) WILD-TYPE |
---|---|---|
Number of samples | 54 | 71 |
Cluster Labels | DEL PEAK 32(19P13.3) MUTATED | DEL PEAK 32(19P13.3) WILD-TYPE |
---|---|---|
Number of samples | 48 | 77 |
Cluster Labels | DEL PEAK 33(22Q13.32) MUTATED | DEL PEAK 33(22Q13.32) WILD-TYPE |
---|---|---|
Number of samples | 48 | 77 |
Cluster Labels | DEL PEAK 34(XP11.3) MUTATED | DEL PEAK 34(XP11.3) WILD-TYPE |
---|---|---|
Number of samples | 36 | 89 |
Cluster Labels | DEL PEAK 35(XQ21.33) MUTATED | DEL PEAK 35(XQ21.33) WILD-TYPE |
---|---|---|
Number of samples | 30 | 95 |
Cluster Labels | DEL PEAK 36(XQ22.3) MUTATED | DEL PEAK 36(XQ22.3) WILD-TYPE |
---|---|---|
Number of samples | 28 | 97 |
-
Cluster data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = BLCA-TP.clin.merged.picked.txt
-
Number of patients = 125
-
Number of clustering approaches = 63
-
Number of selected clinical features = 12
-
Exclude small clusters that include fewer than K patients, 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 two tumor subtypes using 't.test' function in R
For binary clinical features, 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.