This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between subtypes identified by 53 different clustering approaches and 8 clinical features across 68 patients, no significant finding detected with Q value < 0.25.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 1(1p22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 2(1q22) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 3(1q42.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 4(2p24.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 5(2q33.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 6(3q26.31) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 7(4q31.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 8(5p15.33) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 9(5q35.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 10(6p25.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 11(6p21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 12(6q12) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 13(7q21.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 14(8q13.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 15(8q24.13) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 16(10p15.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 17(11q13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 18(12q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 19(13q32.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 20(15q21.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 21(15q26.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 22(17p11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 23(17q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 24(17q25.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 25(19q13.11) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 26(20q13.13) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 1(1p36.32) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 2(2q22.1) 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 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(3p13) 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 5(4q24) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 6(4q35.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 7(5q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 8(6q16.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 9(6q26) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 10(8p23.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 11(9p21.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 12(10p15.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 13(10q23.31) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 14(10q24.33) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 15(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 'Del Peak 16(12p12.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 17(12q24.33) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 18(13q14.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 19(14q23.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 20(15q15.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 21(16q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 22(17p12) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 23(18q21.2) 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 24(19p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 25(22q12.1) 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 26(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 27(Xq27.3) mutation analysis'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
COMPLETENESS OF RESECTION |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
Statistical Tests | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | Chi-square test |
Amp Peak 1(1p22 3) |
0.474 (1.00) |
0.28 (1.00) |
1 (1.00) |
0.274 (1.00) |
0.118 (1.00) |
0.158 (1.00) |
0.0263 (1.00) |
|
Amp Peak 2(1q22) |
0.409 (1.00) |
0.86 (1.00) |
0.551 (1.00) |
1 (1.00) |
0.816 (1.00) |
0.917 (1.00) |
0.445 (1.00) |
|
Amp Peak 3(1q42 3) |
0.211 (1.00) |
0.662 (1.00) |
0.438 (1.00) |
0.764 (1.00) |
0.33 (1.00) |
1 (1.00) |
0.449 (1.00) |
|
Amp Peak 4(2p24 1) |
0.848 (1.00) |
0.953 (1.00) |
0.257 (1.00) |
1 (1.00) |
0.358 (1.00) |
0.921 (1.00) |
0.195 (1.00) |
|
Amp Peak 5(2q33 1) |
0.719 (1.00) |
0.364 (1.00) |
0.0713 (1.00) |
1 (1.00) |
0.135 (1.00) |
0.678 (1.00) |
0.342 (1.00) |
|
Amp Peak 6(3q26 31) |
0.405 (1.00) |
0.656 (1.00) |
0.542 (1.00) |
0.621 (1.00) |
0.0435 (1.00) |
0.755 (1.00) |
0.0868 (1.00) |
|
Amp Peak 7(4q31 3) |
0.635 (1.00) |
0.999 (1.00) |
1 (1.00) |
0.491 (1.00) |
0.727 (1.00) |
0.466 (1.00) |
0.683 (1.00) |
|
Amp Peak 8(5p15 33) |
0.797 (1.00) |
0.903 (1.00) |
1 (1.00) |
0.212 (1.00) |
0.838 (1.00) |
1 (1.00) |
0.727 (1.00) |
|
Amp Peak 9(5q35 3) |
0.648 (1.00) |
0.435 (1.00) |
0.596 (1.00) |
0.518 (1.00) |
0.569 (1.00) |
0.0913 (1.00) |
0.707 (1.00) |
|
Amp Peak 10(6p25 2) |
0.356 (1.00) |
0.961 (1.00) |
1 (1.00) |
0.601 (1.00) |
0.293 (1.00) |
0.788 (1.00) |
0.615 (1.00) |
|
Amp Peak 11(6p21 1) |
0.961 (1.00) |
0.994 (1.00) |
0.799 (1.00) |
0.411 (1.00) |
0.583 (1.00) |
0.838 (1.00) |
0.687 (1.00) |
|
Amp Peak 12(6q12) |
0.976 (1.00) |
0.802 (1.00) |
0.42 (1.00) |
0.0864 (1.00) |
0.429 (1.00) |
0.524 (1.00) |
0.399 (1.00) |
|
Amp Peak 13(7q21 2) |
0.631 (1.00) |
0.103 (1.00) |
0.298 (1.00) |
0.772 (1.00) |
0.562 (1.00) |
0.848 (1.00) |
0.479 (1.00) |
|
Amp Peak 14(8q13 1) |
1 (1.00) |
0.863 (1.00) |
0.128 (1.00) |
0.819 (1.00) |
0.421 (1.00) |
0.843 (1.00) |
0.897 (1.00) |
|
Amp Peak 15(8q24 13) |
0.891 (1.00) |
0.796 (1.00) |
0.128 (1.00) |
1 (1.00) |
0.442 (1.00) |
1 (1.00) |
0.697 (1.00) |
|
Amp Peak 16(10p15 1) |
0.172 (1.00) |
0.93 (1.00) |
0.321 (1.00) |
0.331 (1.00) |
0.0206 (1.00) |
0.902 (1.00) |
0.166 (1.00) |
|
Amp Peak 17(11q13 3) |
0.451 (1.00) |
0.232 (1.00) |
0.734 (1.00) |
0.188 (1.00) |
0.567 (1.00) |
0.0145 (1.00) |
0.0618 (1.00) |
|
Amp Peak 18(12q23 1) |
0.339 (1.00) |
0.391 (1.00) |
1 (1.00) |
0.179 (1.00) |
0.166 (1.00) |
0.252 (1.00) |
0.0892 (1.00) |
|
Amp Peak 19(13q32 3) |
0.185 (1.00) |
0.12 (1.00) |
0.542 (1.00) |
1 (1.00) |
0.145 (1.00) |
0.207 (1.00) |
0.391 (1.00) |
|
Amp Peak 20(15q21 3) |
0.663 (1.00) |
0.25 (1.00) |
0.0961 (1.00) |
0.596 (1.00) |
0.0552 (1.00) |
1 (1.00) |
0.759 (1.00) |
|
Amp Peak 21(15q26 3) |
0.159 (1.00) |
0.911 (1.00) |
0.321 (1.00) |
1 (1.00) |
0.312 (1.00) |
1 (1.00) |
0.793 (1.00) |
|
Amp Peak 22(17p11 2) |
0.107 (1.00) |
0.696 (1.00) |
0.177 (1.00) |
0.567 (1.00) |
0.18 (1.00) |
0.316 (1.00) |
0.869 (1.00) |
|
Amp Peak 23(17q23 1) |
0.492 (1.00) |
0.881 (1.00) |
1 (1.00) |
0.819 (1.00) |
0.643 (1.00) |
0.675 (1.00) |
0.565 (1.00) |
|
Amp Peak 24(17q25 3) |
0.324 (1.00) |
0.432 (1.00) |
0.447 (1.00) |
0.649 (1.00) |
0.866 (1.00) |
0.171 (1.00) |
0.646 (1.00) |
|
Amp Peak 25(19q13 11) |
0.213 (1.00) |
0.631 (1.00) |
0.18 (1.00) |
0.0254 (1.00) |
0.0358 (1.00) |
0.225 (1.00) |
0.0704 (1.00) |
|
Amp Peak 26(20q13 13) |
0.187 (1.00) |
0.106 (1.00) |
0.591 (1.00) |
0.474 (1.00) |
0.0799 (1.00) |
0.0941 (1.00) |
0.0704 (1.00) |
|
Del Peak 1(1p36 32) |
0.432 (1.00) |
0.271 (1.00) |
1 (1.00) |
0.481 (1.00) |
0.643 (1.00) |
0.195 (1.00) |
0.238 (1.00) |
|
Del Peak 2(2q22 1) |
0.368 (1.00) |
0.748 (1.00) |
0.691 (1.00) |
0.709 (1.00) |
0.485 (1.00) |
0.841 (1.00) |
0.734 (1.00) |
|
Del Peak 3(2q37 3) |
0.328 (1.00) |
0.774 (1.00) |
0.741 (1.00) |
0.783 (1.00) |
0.789 (1.00) |
0.902 (1.00) |
0.697 (1.00) |
|
Del Peak 4(3p13) |
0.722 (1.00) |
0.71 (1.00) |
0.0961 (1.00) |
1 (1.00) |
0.58 (1.00) |
0.902 (1.00) |
0.586 (1.00) |
|
Del Peak 5(4q24) |
0.034 (1.00) |
0.264 (1.00) |
0.799 (1.00) |
0.295 (1.00) |
0.537 (1.00) |
0.269 (1.00) |
0.307 (1.00) |
|
Del Peak 6(4q35 1) |
0.0016 (0.594) |
0.116 (1.00) |
0.803 (1.00) |
0.354 (1.00) |
0.677 (1.00) |
0.584 (1.00) |
0.0781 (1.00) |
|
Del Peak 7(5q23 1) |
0.452 (1.00) |
0.894 (1.00) |
0.476 (1.00) |
1 (1.00) |
0.134 (1.00) |
0.502 (1.00) |
0.0211 (1.00) |
|
Del Peak 8(6q16 3) |
0.205 (1.00) |
0.452 (1.00) |
0.796 (1.00) |
0.111 (1.00) |
0.395 (1.00) |
0.624 (1.00) |
0.451 (1.00) |
|
Del Peak 9(6q26) |
0.428 (1.00) |
0.441 (1.00) |
0.794 (1.00) |
0.0253 (1.00) |
0.183 (1.00) |
0.473 (1.00) |
0.73 (1.00) |
|
Del Peak 10(8p23 2) |
0.343 (1.00) |
0.137 (1.00) |
0.298 (1.00) |
1 (1.00) |
0.33 (1.00) |
1 (1.00) |
0.665 (1.00) |
|
Del Peak 11(9p21 3) |
0.0834 (1.00) |
0.518 (1.00) |
1 (1.00) |
0.27 (1.00) |
0.326 (1.00) |
0.327 (1.00) |
0.21 (1.00) |
|
Del Peak 12(10p15 3) |
0.0151 (1.00) |
0.9 (1.00) |
0.289 (1.00) |
0.617 (1.00) |
1 (1.00) |
1 (1.00) |
0.964 (1.00) |
|
Del Peak 13(10q23 31) |
0.739 (1.00) |
0.841 (1.00) |
0.591 (1.00) |
0.478 (1.00) |
1 (1.00) |
0.214 (1.00) |
0.392 (1.00) |
|
Del Peak 14(10q24 33) |
0.384 (1.00) |
0.817 (1.00) |
1 (1.00) |
0.634 (1.00) |
1 (1.00) |
0.338 (1.00) |
0.675 (1.00) |
|
Del Peak 15(11q14 1) |
0.859 (1.00) |
0.0479 (1.00) |
1 (1.00) |
1 (1.00) |
0.0777 (1.00) |
0.59 (1.00) |
0.435 (1.00) |
|
Del Peak 16(12p12 1) |
0.269 (1.00) |
0.422 (1.00) |
1 (1.00) |
0.273 (1.00) |
0.265 (1.00) |
0.153 (1.00) |
0.062 (1.00) |
|
Del Peak 17(12q24 33) |
0.22 (1.00) |
0.163 (1.00) |
0.261 (1.00) |
0.745 (1.00) |
0.75 (1.00) |
0.845 (1.00) |
0.304 (1.00) |
|
Del Peak 18(13q14 2) |
0.177 (1.00) |
0.94 (1.00) |
0.802 (1.00) |
0.481 (1.00) |
1 (1.00) |
0.232 (1.00) |
0.0514 (1.00) |
|
Del Peak 19(14q23 3) |
0.158 (1.00) |
0.839 (1.00) |
1 (1.00) |
0.486 (1.00) |
0.442 (1.00) |
0.492 (1.00) |
0.62 (1.00) |
|
Del Peak 20(15q15 1) |
0.579 (1.00) |
0.211 (1.00) |
0.547 (1.00) |
0.494 (1.00) |
0.289 (1.00) |
0.914 (1.00) |
0.222 (1.00) |
|
Del Peak 21(16q23 1) |
0.12 (1.00) |
0.3 (1.00) |
0.61 (1.00) |
0.409 (1.00) |
0.677 (1.00) |
0.16 (1.00) |
0.51 (1.00) |
|
Del Peak 22(17p12) |
0.22 (1.00) |
0.647 (1.00) |
1 (1.00) |
0.351 (1.00) |
0.446 (1.00) |
0.856 (1.00) |
0.714 (1.00) |
|
Del Peak 23(18q21 2) |
0.0755 (1.00) |
0.139 (1.00) |
0.52 (1.00) |
1 (1.00) |
0.0118 (1.00) |
1 (1.00) |
0.336 (1.00) |
|
Del Peak 24(19p13 3) |
0.73 (1.00) |
0.267 (1.00) |
0.77 (1.00) |
0.279 (1.00) |
0.14 (1.00) |
1 (1.00) |
0.295 (1.00) |
|
Del Peak 25(22q12 1) |
0.535 (1.00) |
0.703 (1.00) |
0.0671 (1.00) |
0.491 (1.00) |
0.606 (1.00) |
0.567 (1.00) |
0.619 (1.00) |
|
Del Peak 26(22q13 32) |
0.678 (1.00) |
0.776 (1.00) |
0.156 (1.00) |
0.47 (1.00) |
0.669 (1.00) |
0.605 (1.00) |
0.354 (1.00) |
|
Del Peak 27(Xq27 3) |
0.0845 (1.00) |
0.933 (1.00) |
0.5 (1.00) |
1 (1.00) |
0.769 (1.00) |
0.522 (1.00) |
0.586 (1.00) |
Cluster Labels | AMP PEAK 1(1P22.3) MUTATED | AMP PEAK 1(1P22.3) WILD-TYPE |
---|---|---|
Number of samples | 19 | 49 |
Cluster Labels | AMP PEAK 2(1Q22) MUTATED | AMP PEAK 2(1Q22) WILD-TYPE |
---|---|---|
Number of samples | 52 | 16 |
Cluster Labels | AMP PEAK 3(1Q42.3) MUTATED | AMP PEAK 3(1Q42.3) WILD-TYPE |
---|---|---|
Number of samples | 44 | 24 |
Cluster Labels | AMP PEAK 4(2P24.1) MUTATED | AMP PEAK 4(2P24.1) WILD-TYPE |
---|---|---|
Number of samples | 17 | 51 |
Cluster Labels | AMP PEAK 5(2Q33.1) MUTATED | AMP PEAK 5(2Q33.1) WILD-TYPE |
---|---|---|
Number of samples | 16 | 52 |
Cluster Labels | AMP PEAK 6(3Q26.31) MUTATED | AMP PEAK 6(3Q26.31) WILD-TYPE |
---|---|---|
Number of samples | 14 | 54 |
Cluster Labels | AMP PEAK 7(4Q31.3) MUTATED | AMP PEAK 7(4Q31.3) WILD-TYPE |
---|---|---|
Number of samples | 8 | 60 |
Cluster Labels | AMP PEAK 8(5P15.33) MUTATED | AMP PEAK 8(5P15.33) WILD-TYPE |
---|---|---|
Number of samples | 32 | 36 |
Cluster Labels | AMP PEAK 9(5Q35.3) MUTATED | AMP PEAK 9(5Q35.3) WILD-TYPE |
---|---|---|
Number of samples | 24 | 44 |
Cluster Labels | AMP PEAK 10(6P25.2) MUTATED | AMP PEAK 10(6P25.2) WILD-TYPE |
---|---|---|
Number of samples | 27 | 41 |
Cluster Labels | AMP PEAK 11(6P21.1) MUTATED | AMP PEAK 11(6P21.1) WILD-TYPE |
---|---|---|
Number of samples | 29 | 39 |
Cluster Labels | AMP PEAK 12(6Q12) MUTATED | AMP PEAK 12(6Q12) WILD-TYPE |
---|---|---|
Number of samples | 21 | 47 |
Cluster Labels | AMP PEAK 13(7Q21.2) MUTATED | AMP PEAK 13(7Q21.2) WILD-TYPE |
---|---|---|
Number of samples | 25 | 43 |
Cluster Labels | AMP PEAK 14(8Q13.1) MUTATED | AMP PEAK 14(8Q13.1) WILD-TYPE |
---|---|---|
Number of samples | 35 | 33 |
Cluster Labels | AMP PEAK 15(8Q24.13) MUTATED | AMP PEAK 15(8Q24.13) WILD-TYPE |
---|---|---|
Number of samples | 40 | 28 |
Cluster Labels | AMP PEAK 16(10P15.1) MUTATED | AMP PEAK 16(10P15.1) WILD-TYPE |
---|---|---|
Number of samples | 12 | 56 |
Cluster Labels | AMP PEAK 17(11Q13.3) MUTATED | AMP PEAK 17(11Q13.3) WILD-TYPE |
---|---|---|
Number of samples | 11 | 57 |
Cluster Labels | AMP PEAK 18(12Q23.1) MUTATED | AMP PEAK 18(12Q23.1) WILD-TYPE |
---|---|---|
Number of samples | 13 | 55 |
Cluster Labels | AMP PEAK 19(13Q32.3) MUTATED | AMP PEAK 19(13Q32.3) WILD-TYPE |
---|---|---|
Number of samples | 14 | 54 |
Cluster Labels | AMP PEAK 20(15Q21.3) MUTATED | AMP PEAK 20(15Q21.3) WILD-TYPE |
---|---|---|
Number of samples | 12 | 56 |
Cluster Labels | AMP PEAK 21(15Q26.3) MUTATED | AMP PEAK 21(15Q26.3) WILD-TYPE |
---|---|---|
Number of samples | 12 | 56 |
Cluster Labels | AMP PEAK 22(17P11.2) MUTATED | AMP PEAK 22(17P11.2) WILD-TYPE |
---|---|---|
Number of samples | 11 | 57 |
Cluster Labels | AMP PEAK 23(17Q23.1) MUTATED | AMP PEAK 23(17Q23.1) WILD-TYPE |
---|---|---|
Number of samples | 33 | 35 |
Cluster Labels | AMP PEAK 24(17Q25.3) MUTATED | AMP PEAK 24(17Q25.3) WILD-TYPE |
---|---|---|
Number of samples | 34 | 34 |
Cluster Labels | AMP PEAK 25(19Q13.11) MUTATED | AMP PEAK 25(19Q13.11) WILD-TYPE |
---|---|---|
Number of samples | 23 | 45 |
Cluster Labels | AMP PEAK 26(20Q13.13) MUTATED | AMP PEAK 26(20Q13.13) WILD-TYPE |
---|---|---|
Number of samples | 22 | 46 |
Cluster Labels | DEL PEAK 1(1P36.32) MUTATED | DEL PEAK 1(1P36.32) WILD-TYPE |
---|---|---|
Number of samples | 32 | 36 |
Cluster Labels | DEL PEAK 2(2Q22.1) MUTATED | DEL PEAK 2(2Q22.1) WILD-TYPE |
---|---|---|
Number of samples | 7 | 61 |
Cluster Labels | DEL PEAK 3(2Q37.3) MUTATED | DEL PEAK 3(2Q37.3) WILD-TYPE |
---|---|---|
Number of samples | 12 | 56 |
Cluster Labels | DEL PEAK 4(3P13) MUTATED | DEL PEAK 4(3P13) WILD-TYPE |
---|---|---|
Number of samples | 12 | 56 |
Cluster Labels | DEL PEAK 5(4Q24) MUTATED | DEL PEAK 5(4Q24) WILD-TYPE |
---|---|---|
Number of samples | 31 | 37 |
Cluster Labels | DEL PEAK 6(4Q35.1) MUTATED | DEL PEAK 6(4Q35.1) WILD-TYPE |
---|---|---|
Number of samples | 30 | 38 |
Cluster Labels | DEL PEAK 7(5Q23.1) MUTATED | DEL PEAK 7(5Q23.1) WILD-TYPE |
---|---|---|
Number of samples | 9 | 59 |
Cluster Labels | DEL PEAK 8(6Q16.3) MUTATED | DEL PEAK 8(6Q16.3) WILD-TYPE |
---|---|---|
Number of samples | 24 | 44 |
Cluster Labels | DEL PEAK 9(6Q26) MUTATED | DEL PEAK 9(6Q26) WILD-TYPE |
---|---|---|
Number of samples | 25 | 43 |
Cluster Labels | DEL PEAK 10(8P23.2) MUTATED | DEL PEAK 10(8P23.2) WILD-TYPE |
---|---|---|
Number of samples | 43 | 25 |
Cluster Labels | DEL PEAK 11(9P21.3) MUTATED | DEL PEAK 11(9P21.3) WILD-TYPE |
---|---|---|
Number of samples | 29 | 39 |
Cluster Labels | DEL PEAK 12(10P15.3) MUTATED | DEL PEAK 12(10P15.3) WILD-TYPE |
---|---|---|
Number of samples | 4 | 64 |
Cluster Labels | DEL PEAK 13(10Q23.31) MUTATED | DEL PEAK 13(10Q23.31) WILD-TYPE |
---|---|---|
Number of samples | 22 | 46 |
Cluster Labels | DEL PEAK 14(10Q24.33) MUTATED | DEL PEAK 14(10Q24.33) WILD-TYPE |
---|---|---|
Number of samples | 19 | 49 |
Cluster Labels | DEL PEAK 15(11Q14.1) MUTATED | DEL PEAK 15(11Q14.1) WILD-TYPE |
---|---|---|
Number of samples | 14 | 54 |
Cluster Labels | DEL PEAK 16(12P12.1) MUTATED | DEL PEAK 16(12P12.1) WILD-TYPE |
---|---|---|
Number of samples | 13 | 55 |
Cluster Labels | DEL PEAK 17(12Q24.33) MUTATED | DEL PEAK 17(12Q24.33) WILD-TYPE |
---|---|---|
Number of samples | 9 | 59 |
Cluster Labels | DEL PEAK 18(13Q14.2) MUTATED | DEL PEAK 18(13Q14.2) WILD-TYPE |
---|---|---|
Number of samples | 32 | 36 |
Cluster Labels | DEL PEAK 19(14Q23.3) MUTATED | DEL PEAK 19(14Q23.3) WILD-TYPE |
---|---|---|
Number of samples | 27 | 41 |
Cluster Labels | DEL PEAK 20(15Q15.1) MUTATED | DEL PEAK 20(15Q15.1) WILD-TYPE |
---|---|---|
Number of samples | 15 | 53 |
Cluster Labels | DEL PEAK 21(16Q23.1) MUTATED | DEL PEAK 21(16Q23.1) WILD-TYPE |
---|---|---|
Number of samples | 30 | 38 |
Cluster Labels | DEL PEAK 22(17P12) MUTATED | DEL PEAK 22(17P12) WILD-TYPE |
---|---|---|
Number of samples | 41 | 27 |
Cluster Labels | DEL PEAK 23(18Q21.2) MUTATED | DEL PEAK 23(18Q21.2) WILD-TYPE |
---|---|---|
Number of samples | 13 | 55 |
Cluster Labels | DEL PEAK 24(19P13.3) MUTATED | DEL PEAK 24(19P13.3) WILD-TYPE |
---|---|---|
Number of samples | 17 | 51 |
Cluster Labels | DEL PEAK 25(22Q12.1) MUTATED | DEL PEAK 25(22Q12.1) WILD-TYPE |
---|---|---|
Number of samples | 14 | 54 |
Cluster Labels | DEL PEAK 26(22Q13.32) MUTATED | DEL PEAK 26(22Q13.32) WILD-TYPE |
---|---|---|
Number of samples | 18 | 50 |
Cluster Labels | DEL PEAK 27(XQ27.3) MUTATED | DEL PEAK 27(XQ27.3) WILD-TYPE |
---|---|---|
Number of samples | 11 | 57 |
-
Cluster data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = LIHC-TP.clin.merged.picked.txt
-
Number of patients = 68
-
Number of clustering approaches = 53
-
Number of selected clinical features = 8
-
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.