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 9 clinical features across 846 patients, 3 significant findings detected with Q value < 0.25.
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2 subtypes identified in current cancer cohort by 'Amp Peak 1(1p22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
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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(1q44) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 4(3p26.1) 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(4q13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 7(6p23) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 8(6q21) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 9(8p11.23) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 10(8p11.21) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 11(8q24.21) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 12(10p15.1) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 13(10q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 14(11p13) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 15(11q13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 16(11q14.1) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 17(12p13.33) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 18(12q15) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 19(13q12.3) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 20(13q34) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 21(14q21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 22(15q26.3) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 23(17p11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 24(17q12) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 25(17q23.1) mutation analysis'. These subtypes correlate to 'GENDER'.
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2 subtypes identified in current cancer cohort by 'Amp Peak 26(19q12) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 27(19q13.42) mutation analysis'. These subtypes do not correlate to any clinical features.
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2 subtypes identified in current cancer cohort by 'Amp Peak 28(20q13.2) 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 1(1p36.13) 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 2(1p21.2) 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 3(2q37.3) 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 4(3p14.3) mutation analysis'. These subtypes correlate to 'AGE'.
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2 subtypes identified in current cancer cohort by 'Del Peak 5(4p16.3) 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 6(4q35.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 7(5q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 8(5q21.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 9(6p25.3) 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 10(6q15) 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 11(6q27) mutation analysis'. These subtypes correlate to 'AGE'.
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2 subtypes identified in current cancer cohort by 'Del Peak 12(7p22.3) 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 13(7q36.1) 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 14(8p23.2) 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 15(8p11.21) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 16(9p21.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 17(9q21.11) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 18(10q23.31) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 19(10q26.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 20(11p15.5) 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 21(11q23.2) 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 22(12p13.1) 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 23(12q24.31) 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(14q24.3) 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 26(15q13.1) 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 27(16q24.3) 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 28(17p12) 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 29(17q21.31) 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 30(18q23) 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 31(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 32(19q13.32) 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 33(20p13) 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(21q11.2) 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 35(22q13.32) mutation analysis'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
RADIATIONS RADIATION REGIMENINDICATION |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
Statistical Tests | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | t-test | t-test | Chi-square test |
Amp Peak 1(1p22 3) |
0.982 (1.00) |
0.834 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.542 (1.00) |
0.429 (1.00) |
0.103 (1.00) |
0.613 (1.00) |
|
Amp Peak 2(1q21 3) |
0.807 (1.00) |
0.509 (1.00) |
0.278 (1.00) |
0.153 (1.00) |
0.447 (1.00) |
0.474 (1.00) |
0.654 (1.00) |
0.375 (1.00) |
|
Amp Peak 3(1q44) |
0.0119 (1.00) |
0.872 (1.00) |
0.717 (1.00) |
0.372 (1.00) |
0.34 (1.00) |
0.216 (1.00) |
0.671 (1.00) |
0.453 (1.00) |
|
Amp Peak 4(3p26 1) |
0.00479 (1.00) |
0.501 (1.00) |
0.217 (1.00) |
0.844 (1.00) |
0.103 (1.00) |
0.108 (1.00) |
0.569 (1.00) |
0.172 (1.00) |
|
Amp Peak 5(3q26 32) |
0.629 (1.00) |
0.304 (1.00) |
0.726 (1.00) |
0.123 (1.00) |
0.329 (1.00) |
0.864 (1.00) |
0.703 (1.00) |
0.626 (1.00) |
|
Amp Peak 6(4q13 3) |
0.00223 (1.00) |
0.382 (1.00) |
1 (1.00) |
1 (1.00) |
0.849 (1.00) |
0.281 (1.00) |
0.358 (1.00) |
0.135 (1.00) |
|
Amp Peak 7(6p23) |
0.633 (1.00) |
0.345 (1.00) |
0.458 (1.00) |
0.362 (1.00) |
0.919 (1.00) |
0.122 (1.00) |
0.258 (1.00) |
0.595 (1.00) |
|
Amp Peak 8(6q21) |
0.0119 (1.00) |
0.553 (1.00) |
1 (1.00) |
0.535 (1.00) |
0.956 (1.00) |
0.806 (1.00) |
0.942 (1.00) |
0.391 (1.00) |
|
Amp Peak 9(8p11 23) |
0.0277 (1.00) |
0.0884 (1.00) |
0.165 (1.00) |
0.804 (1.00) |
0.0945 (1.00) |
0.143 (1.00) |
0.0108 (1.00) |
0.015 (1.00) |
|
Amp Peak 10(8p11 21) |
0.84 (1.00) |
0.0401 (1.00) |
0.165 (1.00) |
0.0395 (1.00) |
0.868 (1.00) |
0.539 (1.00) |
0.573 (1.00) |
0.316 (1.00) |
|
Amp Peak 11(8q24 21) |
0.118 (1.00) |
0.146 (1.00) |
0.507 (1.00) |
0.613 (1.00) |
0.535 (1.00) |
0.0554 (1.00) |
0.18 (1.00) |
0.496 (1.00) |
|
Amp Peak 12(10p15 1) |
0.204 (1.00) |
0.653 (1.00) |
0.0667 (1.00) |
0.248 (1.00) |
0.902 (1.00) |
0.824 (1.00) |
0.987 (1.00) |
0.412 (1.00) |
|
Amp Peak 13(10q22 3) |
0.116 (1.00) |
0.94 (1.00) |
1 (1.00) |
0.576 (1.00) |
0.218 (1.00) |
0.692 (1.00) |
0.66 (1.00) |
0.343 (1.00) |
|
Amp Peak 14(11p13) |
0.462 (1.00) |
0.791 (1.00) |
1 (1.00) |
0.378 (1.00) |
0.616 (1.00) |
0.544 (1.00) |
0.794 (1.00) |
0.196 (1.00) |
|
Amp Peak 15(11q13 3) |
0.241 (1.00) |
0.297 (1.00) |
0.32 (1.00) |
0.68 (1.00) |
0.692 (1.00) |
0.729 (1.00) |
0.433 (1.00) |
0.225 (1.00) |
|
Amp Peak 16(11q14 1) |
0.0937 (1.00) |
0.347 (1.00) |
0.698 (1.00) |
0.781 (1.00) |
0.466 (1.00) |
0.712 (1.00) |
0.334 (1.00) |
0.394 (1.00) |
|
Amp Peak 17(12p13 33) |
0.802 (1.00) |
0.627 (1.00) |
0.459 (1.00) |
0.0815 (1.00) |
0.71 (1.00) |
0.279 (1.00) |
0.785 (1.00) |
0.171 (1.00) |
|
Amp Peak 18(12q15) |
0.0388 (1.00) |
0.253 (1.00) |
0.0127 (1.00) |
0.927 (1.00) |
0.41 (1.00) |
0.0544 (1.00) |
0.196 (1.00) |
0.0911 (1.00) |
|
Amp Peak 19(13q12 3) |
0.0366 (1.00) |
0.28 (1.00) |
0.627 (1.00) |
0.364 (1.00) |
0.257 (1.00) |
0.185 (1.00) |
0.628 (1.00) |
0.581 (1.00) |
|
Amp Peak 20(13q34) |
0.977 (1.00) |
0.104 (1.00) |
0.372 (1.00) |
0.916 (1.00) |
0.557 (1.00) |
0.126 (1.00) |
0.818 (1.00) |
0.238 (1.00) |
|
Amp Peak 21(14q21 1) |
0.429 (1.00) |
0.0405 (1.00) |
0.694 (1.00) |
0.843 (1.00) |
0.585 (1.00) |
0.00868 (1.00) |
0.0535 (1.00) |
0.0634 (1.00) |
|
Amp Peak 22(15q26 3) |
0.214 (1.00) |
0.0404 (1.00) |
0.0654 (1.00) |
0.679 (1.00) |
0.134 (1.00) |
0.701 (1.00) |
0.633 (1.00) |
0.811 (1.00) |
|
Amp Peak 23(17p11 2) |
0.133 (1.00) |
0.135 (1.00) |
0.118 (1.00) |
0.0628 (1.00) |
0.692 (1.00) |
0.333 (1.00) |
0.488 (1.00) |
0.27 (1.00) |
|
Amp Peak 24(17q12) |
0.175 (1.00) |
0.658 (1.00) |
0.000793 (0.395) |
0.932 (1.00) |
0.724 (1.00) |
0.0306 (1.00) |
0.355 (1.00) |
0.232 (1.00) |
|
Amp Peak 25(17q23 1) |
0.0678 (1.00) |
0.871 (1.00) |
0.000343 (0.172) |
0.29 (1.00) |
0.183 (1.00) |
0.435 (1.00) |
0.753 (1.00) |
0.0669 (1.00) |
|
Amp Peak 26(19q12) |
0.4 (1.00) |
0.467 (1.00) |
0.701 (1.00) |
0.168 (1.00) |
0.176 (1.00) |
0.0905 (1.00) |
0.45 (1.00) |
0.683 (1.00) |
|
Amp Peak 27(19q13 42) |
0.643 (1.00) |
0.266 (1.00) |
0.258 (1.00) |
0.526 (1.00) |
0.179 (1.00) |
0.572 (1.00) |
0.84 (1.00) |
0.932 (1.00) |
|
Amp Peak 28(20q13 2) |
0.69 (1.00) |
0.32 (1.00) |
0.181 (1.00) |
0.0442 (1.00) |
0.554 (1.00) |
0.257 (1.00) |
0.35 (1.00) |
0.329 (1.00) |
|
Del Peak 1(1p36 13) |
0.208 (1.00) |
0.415 (1.00) |
0.18 (1.00) |
0.808 (1.00) |
0.373 (1.00) |
0.0863 (1.00) |
0.0328 (1.00) |
0.0292 (1.00) |
|
Del Peak 2(1p21 2) |
0.0629 (1.00) |
0.132 (1.00) |
1 (1.00) |
0.554 (1.00) |
0.779 (1.00) |
0.016 (1.00) |
0.0302 (1.00) |
0.0302 (1.00) |
|
Del Peak 3(2q37 3) |
0.887 (1.00) |
0.992 (1.00) |
0.294 (1.00) |
0.539 (1.00) |
0.56 (1.00) |
0.452 (1.00) |
0.495 (1.00) |
0.605 (1.00) |
|
Del Peak 4(3p14 3) |
0.0195 (1.00) |
9.72e-05 (0.049) |
1 (1.00) |
0.665 (1.00) |
0.437 (1.00) |
0.733 (1.00) |
0.946 (1.00) |
0.818 (1.00) |
|
Del Peak 5(4p16 3) |
0.833 (1.00) |
0.0841 (1.00) |
0.727 (1.00) |
0.665 (1.00) |
0.94 (1.00) |
0.86 (1.00) |
0.829 (1.00) |
0.487 (1.00) |
|
Del Peak 6(4q35 2) |
0.112 (1.00) |
0.717 (1.00) |
0.286 (1.00) |
0.863 (1.00) |
0.214 (1.00) |
0.448 (1.00) |
0.941 (1.00) |
0.932 (1.00) |
|
Del Peak 7(5q11 2) |
0.232 (1.00) |
0.00986 (1.00) |
0.459 (1.00) |
0.521 (1.00) |
0.313 (1.00) |
0.599 (1.00) |
0.269 (1.00) |
0.526 (1.00) |
|
Del Peak 8(5q21 3) |
0.349 (1.00) |
0.0173 (1.00) |
0.122 (1.00) |
1 (1.00) |
0.627 (1.00) |
0.273 (1.00) |
0.000681 (0.34) |
0.319 (1.00) |
|
Del Peak 9(6p25 3) |
0.566 (1.00) |
0.0621 (1.00) |
0.68 (1.00) |
0.258 (1.00) |
0.832 (1.00) |
0.397 (1.00) |
0.0282 (1.00) |
0.602 (1.00) |
|
Del Peak 10(6q15) |
0.405 (1.00) |
0.105 (1.00) |
0.725 (1.00) |
0.865 (1.00) |
0.538 (1.00) |
0.462 (1.00) |
0.132 (1.00) |
0.278 (1.00) |
|
Del Peak 11(6q27) |
0.132 (1.00) |
0.000124 (0.0623) |
0.177 (1.00) |
0.498 (1.00) |
0.254 (1.00) |
0.354 (1.00) |
0.345 (1.00) |
0.599 (1.00) |
|
Del Peak 12(7p22 3) |
0.107 (1.00) |
0.339 (1.00) |
0.617 (1.00) |
0.725 (1.00) |
0.857 (1.00) |
0.793 (1.00) |
0.0331 (1.00) |
0.0272 (1.00) |
|
Del Peak 13(7q36 1) |
0.0181 (1.00) |
0.916 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.275 (1.00) |
0.861 (1.00) |
0.782 (1.00) |
0.923 (1.00) |
|
Del Peak 14(8p23 2) |
0.276 (1.00) |
0.646 (1.00) |
0.513 (1.00) |
0.198 (1.00) |
0.729 (1.00) |
0.12 (1.00) |
0.718 (1.00) |
0.991 (1.00) |
|
Del Peak 15(8p11 21) |
0.0141 (1.00) |
0.367 (1.00) |
0.219 (1.00) |
0.684 (1.00) |
0.501 (1.00) |
0.0254 (1.00) |
0.21 (1.00) |
0.544 (1.00) |
|
Del Peak 16(9p21 3) |
0.0298 (1.00) |
0.607 (1.00) |
0.288 (1.00) |
0.128 (1.00) |
0.16 (1.00) |
0.000571 (0.285) |
0.108 (1.00) |
0.00122 (0.606) |
|
Del Peak 17(9q21 11) |
0.506 (1.00) |
0.929 (1.00) |
0.268 (1.00) |
0.857 (1.00) |
0.333 (1.00) |
0.381 (1.00) |
0.659 (1.00) |
0.399 (1.00) |
|
Del Peak 18(10q23 31) |
0.868 (1.00) |
0.58 (1.00) |
0.0659 (1.00) |
0.48 (1.00) |
0.872 (1.00) |
0.362 (1.00) |
0.858 (1.00) |
0.601 (1.00) |
|
Del Peak 19(10q26 3) |
0.0426 (1.00) |
0.834 (1.00) |
0.46 (1.00) |
0.792 (1.00) |
0.586 (1.00) |
0.282 (1.00) |
0.548 (1.00) |
0.562 (1.00) |
|
Del Peak 20(11p15 5) |
0.271 (1.00) |
0.797 (1.00) |
0.461 (1.00) |
0.93 (1.00) |
0.979 (1.00) |
0.641 (1.00) |
0.122 (1.00) |
0.673 (1.00) |
|
Del Peak 21(11q23 2) |
0.365 (1.00) |
0.346 (1.00) |
0.177 (1.00) |
0.936 (1.00) |
0.24 (1.00) |
0.142 (1.00) |
0.517 (1.00) |
0.257 (1.00) |
|
Del Peak 22(12p13 1) |
0.573 (1.00) |
0.623 (1.00) |
0.666 (1.00) |
0.529 (1.00) |
0.0576 (1.00) |
0.395 (1.00) |
0.52 (1.00) |
0.292 (1.00) |
|
Del Peak 23(12q24 31) |
0.243 (1.00) |
0.372 (1.00) |
0.372 (1.00) |
0.597 (1.00) |
0.852 (1.00) |
0.359 (1.00) |
0.678 (1.00) |
0.783 (1.00) |
|
Del Peak 24(13q14 2) |
0.0658 (1.00) |
0.763 (1.00) |
0.74 (1.00) |
0.573 (1.00) |
0.941 (1.00) |
0.425 (1.00) |
0.154 (1.00) |
0.972 (1.00) |
|
Del Peak 25(14q24 3) |
0.174 (1.00) |
0.88 (1.00) |
1 (1.00) |
0.667 (1.00) |
0.74 (1.00) |
0.0848 (1.00) |
0.807 (1.00) |
0.874 (1.00) |
|
Del Peak 26(15q13 1) |
0.412 (1.00) |
0.212 (1.00) |
1 (1.00) |
0.736 (1.00) |
0.225 (1.00) |
0.147 (1.00) |
0.803 (1.00) |
0.389 (1.00) |
|
Del Peak 27(16q24 3) |
0.115 (1.00) |
0.000886 (0.44) |
1 (1.00) |
0.614 (1.00) |
0.176 (1.00) |
0.268 (1.00) |
0.413 (1.00) |
0.263 (1.00) |
|
Del Peak 28(17p12) |
0.147 (1.00) |
0.00382 (1.00) |
0.495 (1.00) |
0.681 (1.00) |
0.908 (1.00) |
0.0151 (1.00) |
0.24 (1.00) |
0.546 (1.00) |
|
Del Peak 29(17q21 31) |
0.597 (1.00) |
0.00051 (0.255) |
0.17 (1.00) |
0.737 (1.00) |
0.312 (1.00) |
0.0512 (1.00) |
0.135 (1.00) |
0.232 (1.00) |
|
Del Peak 30(18q23) |
0.0228 (1.00) |
0.574 (1.00) |
1 (1.00) |
0.199 (1.00) |
0.511 (1.00) |
0.045 (1.00) |
0.184 (1.00) |
0.206 (1.00) |
|
Del Peak 31(19p13 3) |
0.415 (1.00) |
0.0347 (1.00) |
0.726 (1.00) |
0.448 (1.00) |
0.972 (1.00) |
0.654 (1.00) |
0.181 (1.00) |
0.909 (1.00) |
|
Del Peak 32(19q13 32) |
0.857 (1.00) |
0.758 (1.00) |
0.694 (1.00) |
0.843 (1.00) |
0.149 (1.00) |
0.174 (1.00) |
0.935 (1.00) |
0.417 (1.00) |
|
Del Peak 33(20p13) |
0.0125 (1.00) |
0.469 (1.00) |
0.63 (1.00) |
0.259 (1.00) |
0.707 (1.00) |
0.972 (1.00) |
0.782 (1.00) |
0.25 (1.00) |
|
Del Peak 34(21q11 2) |
0.338 (1.00) |
0.485 (1.00) |
0.217 (1.00) |
0.323 (1.00) |
0.452 (1.00) |
0.217 (1.00) |
0.619 (1.00) |
0.0136 (1.00) |
|
Del Peak 35(22q13 32) |
0.491 (1.00) |
0.563 (1.00) |
0.525 (1.00) |
0.0524 (1.00) |
0.779 (1.00) |
0.133 (1.00) |
0.848 (1.00) |
0.82 (1.00) |
Cluster Labels | AMP PEAK 1(1P22.3) MUTATED | AMP PEAK 1(1P22.3) WILD-TYPE |
---|---|---|
Number of samples | 186 | 660 |
Cluster Labels | AMP PEAK 2(1Q21.3) MUTATED | AMP PEAK 2(1Q21.3) WILD-TYPE |
---|---|---|
Number of samples | 608 | 238 |
Cluster Labels | AMP PEAK 3(1Q44) MUTATED | AMP PEAK 3(1Q44) WILD-TYPE |
---|---|---|
Number of samples | 608 | 238 |
Cluster Labels | AMP PEAK 4(3P26.1) MUTATED | AMP PEAK 4(3P26.1) WILD-TYPE |
---|---|---|
Number of samples | 178 | 668 |
Cluster Labels | AMP PEAK 5(3Q26.32) MUTATED | AMP PEAK 5(3Q26.32) WILD-TYPE |
---|---|---|
Number of samples | 276 | 570 |
Cluster Labels | AMP PEAK 6(4Q13.3) MUTATED | AMP PEAK 6(4Q13.3) WILD-TYPE |
---|---|---|
Number of samples | 138 | 708 |
Cluster Labels | AMP PEAK 7(6P23) MUTATED | AMP PEAK 7(6P23) WILD-TYPE |
---|---|---|
Number of samples | 223 | 623 |
Cluster Labels | AMP PEAK 8(6Q21) MUTATED | AMP PEAK 8(6Q21) WILD-TYPE |
---|---|---|
Number of samples | 157 | 689 |
Cluster Labels | AMP PEAK 9(8P11.23) MUTATED | AMP PEAK 9(8P11.23) WILD-TYPE |
---|---|---|
Number of samples | 324 | 522 |
Cluster Labels | AMP PEAK 10(8P11.21) MUTATED | AMP PEAK 10(8P11.21) WILD-TYPE |
---|---|---|
Number of samples | 329 | 517 |
Cluster Labels | AMP PEAK 11(8Q24.21) MUTATED | AMP PEAK 11(8Q24.21) WILD-TYPE |
---|---|---|
Number of samples | 550 | 296 |
Cluster Labels | AMP PEAK 12(10P15.1) MUTATED | AMP PEAK 12(10P15.1) WILD-TYPE |
---|---|---|
Number of samples | 242 | 604 |
Cluster Labels | AMP PEAK 13(10Q22.3) MUTATED | AMP PEAK 13(10Q22.3) WILD-TYPE |
---|---|---|
Number of samples | 127 | 719 |
Cluster Labels | AMP PEAK 14(11P13) MUTATED | AMP PEAK 14(11P13) WILD-TYPE |
---|---|---|
Number of samples | 180 | 666 |
Cluster Labels | AMP PEAK 15(11Q13.3) MUTATED | AMP PEAK 15(11Q13.3) WILD-TYPE |
---|---|---|
Number of samples | 328 | 518 |
Cluster Labels | AMP PEAK 16(11Q14.1) MUTATED | AMP PEAK 16(11Q14.1) WILD-TYPE |
---|---|---|
Number of samples | 212 | 634 |
Cluster Labels | AMP PEAK 17(12P13.33) MUTATED | AMP PEAK 17(12P13.33) WILD-TYPE |
---|---|---|
Number of samples | 220 | 626 |
Cluster Labels | AMP PEAK 18(12Q15) MUTATED | AMP PEAK 18(12Q15) WILD-TYPE |
---|---|---|
Number of samples | 223 | 623 |
Cluster Labels | AMP PEAK 19(13Q12.3) MUTATED | AMP PEAK 19(13Q12.3) WILD-TYPE |
---|---|---|
Number of samples | 124 | 722 |
Cluster Labels | AMP PEAK 20(13Q34) MUTATED | AMP PEAK 20(13Q34) WILD-TYPE |
---|---|---|
Number of samples | 147 | 699 |
Cluster Labels | AMP PEAK 21(14Q21.1) MUTATED | AMP PEAK 21(14Q21.1) WILD-TYPE |
---|---|---|
Number of samples | 175 | 671 |
Cluster Labels | AMP PEAK 22(15Q26.3) MUTATED | AMP PEAK 22(15Q26.3) WILD-TYPE |
---|---|---|
Number of samples | 156 | 690 |
Cluster Labels | AMP PEAK 23(17P11.2) MUTATED | AMP PEAK 23(17P11.2) WILD-TYPE |
---|---|---|
Number of samples | 118 | 728 |
Cluster Labels | AMP PEAK 24(17Q12) MUTATED | AMP PEAK 24(17Q12) WILD-TYPE |
---|---|---|
Number of samples | 277 | 569 |
Cluster Labels | AMP PEAK 25(17Q23.1) MUTATED | AMP PEAK 25(17Q23.1) WILD-TYPE |
---|---|---|
Number of samples | 351 | 495 |
P value = 0.000343 (Fisher's exact test), Q value = 0.17
nPatients | FEMALE | MALE |
---|---|---|
ALL | 837 | 9 |
AMP PEAK 25(17Q23.1) MUTATED | 342 | 9 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 495 | 0 |
Cluster Labels | AMP PEAK 26(19Q12) MUTATED | AMP PEAK 26(19Q12) WILD-TYPE |
---|---|---|
Number of samples | 217 | 629 |
Cluster Labels | AMP PEAK 27(19Q13.42) MUTATED | AMP PEAK 27(19Q13.42) WILD-TYPE |
---|---|---|
Number of samples | 226 | 620 |
Cluster Labels | AMP PEAK 28(20Q13.2) MUTATED | AMP PEAK 28(20Q13.2) WILD-TYPE |
---|---|---|
Number of samples | 440 | 406 |
Cluster Labels | DEL PEAK 1(1P36.13) MUTATED | DEL PEAK 1(1P36.13) WILD-TYPE |
---|---|---|
Number of samples | 359 | 487 |
Cluster Labels | DEL PEAK 2(1P21.2) MUTATED | DEL PEAK 2(1P21.2) WILD-TYPE |
---|---|---|
Number of samples | 290 | 556 |
Cluster Labels | DEL PEAK 3(2Q37.3) MUTATED | DEL PEAK 3(2Q37.3) WILD-TYPE |
---|---|---|
Number of samples | 251 | 595 |
Cluster Labels | DEL PEAK 4(3P14.3) MUTATED | DEL PEAK 4(3P14.3) WILD-TYPE |
---|---|---|
Number of samples | 266 | 580 |
P value = 9.72e-05 (t-test), Q value = 0.049
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 845 | 58.5 (13.2) |
DEL PEAK 4(3P14.3) MUTATED | 266 | 55.9 (13.2) |
DEL PEAK 4(3P14.3) WILD-TYPE | 579 | 59.7 (13.1) |
Cluster Labels | DEL PEAK 5(4P16.3) MUTATED | DEL PEAK 5(4P16.3) WILD-TYPE |
---|---|---|
Number of samples | 266 | 580 |
Cluster Labels | DEL PEAK 6(4Q35.2) MUTATED | DEL PEAK 6(4Q35.2) WILD-TYPE |
---|---|---|
Number of samples | 266 | 580 |
Cluster Labels | DEL PEAK 7(5Q11.2) MUTATED | DEL PEAK 7(5Q11.2) WILD-TYPE |
---|---|---|
Number of samples | 220 | 626 |
Cluster Labels | DEL PEAK 8(5Q21.3) MUTATED | DEL PEAK 8(5Q21.3) WILD-TYPE |
---|---|---|
Number of samples | 212 | 634 |
Cluster Labels | DEL PEAK 9(6P25.3) MUTATED | DEL PEAK 9(6P25.3) WILD-TYPE |
---|---|---|
Number of samples | 159 | 687 |
Cluster Labels | DEL PEAK 10(6Q15) MUTATED | DEL PEAK 10(6Q15) WILD-TYPE |
---|---|---|
Number of samples | 284 | 562 |
Cluster Labels | DEL PEAK 11(6Q27) MUTATED | DEL PEAK 11(6Q27) WILD-TYPE |
---|---|---|
Number of samples | 289 | 557 |
P value = 0.000124 (t-test), Q value = 0.062
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 845 | 58.5 (13.2) |
DEL PEAK 11(6Q27) MUTATED | 289 | 56.1 (12.8) |
DEL PEAK 11(6Q27) WILD-TYPE | 556 | 59.8 (13.3) |
Cluster Labels | DEL PEAK 12(7P22.3) MUTATED | DEL PEAK 12(7P22.3) WILD-TYPE |
---|---|---|
Number of samples | 114 | 732 |
Cluster Labels | DEL PEAK 13(7Q36.1) MUTATED | DEL PEAK 13(7Q36.1) WILD-TYPE |
---|---|---|
Number of samples | 172 | 674 |
Cluster Labels | DEL PEAK 14(8P23.2) MUTATED | DEL PEAK 14(8P23.2) WILD-TYPE |
---|---|---|
Number of samples | 449 | 397 |
Cluster Labels | DEL PEAK 15(8P11.21) MUTATED | DEL PEAK 15(8P11.21) WILD-TYPE |
---|---|---|
Number of samples | 163 | 683 |
Cluster Labels | DEL PEAK 16(9P21.3) MUTATED | DEL PEAK 16(9P21.3) WILD-TYPE |
---|---|---|
Number of samples | 291 | 555 |
Cluster Labels | DEL PEAK 17(9Q21.11) MUTATED | DEL PEAK 17(9Q21.11) WILD-TYPE |
---|---|---|
Number of samples | 232 | 614 |
Cluster Labels | DEL PEAK 18(10Q23.31) MUTATED | DEL PEAK 18(10Q23.31) WILD-TYPE |
---|---|---|
Number of samples | 245 | 601 |
Cluster Labels | DEL PEAK 19(10Q26.3) MUTATED | DEL PEAK 19(10Q26.3) WILD-TYPE |
---|---|---|
Number of samples | 247 | 599 |
Cluster Labels | DEL PEAK 20(11P15.5) MUTATED | DEL PEAK 20(11P15.5) WILD-TYPE |
---|---|---|
Number of samples | 249 | 597 |
Cluster Labels | DEL PEAK 21(11Q23.2) MUTATED | DEL PEAK 21(11Q23.2) WILD-TYPE |
---|---|---|
Number of samples | 423 | 423 |
Cluster Labels | DEL PEAK 22(12P13.1) MUTATED | DEL PEAK 22(12P13.1) WILD-TYPE |
---|---|---|
Number of samples | 151 | 695 |
Cluster Labels | DEL PEAK 23(12Q24.31) MUTATED | DEL PEAK 23(12Q24.31) WILD-TYPE |
---|---|---|
Number of samples | 147 | 699 |
Cluster Labels | DEL PEAK 24(13Q14.2) MUTATED | DEL PEAK 24(13Q14.2) WILD-TYPE |
---|---|---|
Number of samples | 391 | 455 |
Cluster Labels | DEL PEAK 25(14Q24.3) MUTATED | DEL PEAK 25(14Q24.3) WILD-TYPE |
---|---|---|
Number of samples | 271 | 575 |
Cluster Labels | DEL PEAK 26(15Q13.1) MUTATED | DEL PEAK 26(15Q13.1) WILD-TYPE |
---|---|---|
Number of samples | 297 | 549 |
Cluster Labels | DEL PEAK 27(16Q24.3) MUTATED | DEL PEAK 27(16Q24.3) WILD-TYPE |
---|---|---|
Number of samples | 548 | 298 |
Cluster Labels | DEL PEAK 28(17P12) MUTATED | DEL PEAK 28(17P12) WILD-TYPE |
---|---|---|
Number of samples | 513 | 333 |
Cluster Labels | DEL PEAK 29(17Q21.31) MUTATED | DEL PEAK 29(17Q21.31) WILD-TYPE |
---|---|---|
Number of samples | 300 | 546 |
Cluster Labels | DEL PEAK 30(18Q23) MUTATED | DEL PEAK 30(18Q23) WILD-TYPE |
---|---|---|
Number of samples | 278 | 568 |
Cluster Labels | DEL PEAK 31(19P13.3) MUTATED | DEL PEAK 31(19P13.3) WILD-TYPE |
---|---|---|
Number of samples | 293 | 553 |
Cluster Labels | DEL PEAK 32(19Q13.32) MUTATED | DEL PEAK 32(19Q13.32) WILD-TYPE |
---|---|---|
Number of samples | 174 | 672 |
Cluster Labels | DEL PEAK 33(20P13) MUTATED | DEL PEAK 33(20P13) WILD-TYPE |
---|---|---|
Number of samples | 126 | 720 |
Cluster Labels | DEL PEAK 34(21Q11.2) MUTATED | DEL PEAK 34(21Q11.2) WILD-TYPE |
---|---|---|
Number of samples | 175 | 671 |
Cluster Labels | DEL PEAK 35(22Q13.32) MUTATED | DEL PEAK 35(22Q13.32) WILD-TYPE |
---|---|---|
Number of samples | 380 | 466 |
-
Cluster data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = BRCA-TP.clin.merged.picked.txt
-
Number of patients = 846
-
Number of clustering approaches = 63
-
Number of selected clinical features = 9
-
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.