This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between subtypes identified by 43 different clustering approaches and 6 clinical features across 207 patients, 15 significant findings detected with Q value < 0.25.
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2 subtypes identified in current cancer cohort by 'Amp Peak 1(1q32.1) mutation analysis'. These subtypes correlate to 'AGE'.
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2 subtypes identified in current cancer cohort by 'Amp Peak 2(4q12) 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 3(7p11.2) mutation analysis'. These subtypes correlate to 'AGE'.
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2 subtypes identified in current cancer cohort by 'Amp Peak 4(7q32.3) mutation analysis'. These subtypes correlate to 'AGE'.
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2 subtypes identified in current cancer cohort by 'Amp Peak 5(8q24.21) 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 6(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 7(10q11.21) 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 8(11q23.3) 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 9(12p13.32) 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(12p11.22) 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(12q14.1) mutation analysis'. These subtypes correlate to 'Time to Death'.
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2 subtypes identified in current cancer cohort by 'Amp Peak 12(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 'Amp Peak 13(19q13.2) mutation analysis'. These subtypes correlate to 'Time to Death' and 'AGE'.
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2 subtypes identified in current cancer cohort by 'Amp Peak 14(Xp22.33) 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 15(Xq11.2) 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(1p36.31) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
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2 subtypes identified in current cancer cohort by 'Del Peak 2(1p32.3) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE' and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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2 subtypes identified in current cancer cohort by 'Del Peak 3(1q43) 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(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 5(3p21.1) 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 6(3q29) 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 7(4q33) 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 8(4q35.2) 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 9(5q35.2) 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 10(6p24.1) 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 11(6q24.3) 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 12(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 13(9p21.3) mutation analysis'. These subtypes correlate to 'Time to Death', 'AGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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2 subtypes identified in current cancer cohort by 'Del Peak 14(10q26.2) mutation analysis'. These subtypes correlate to 'Time to Death'.
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2 subtypes identified in current cancer cohort by 'Del Peak 15(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 16(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 17(12q24.11) 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 18(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 19(13q34) 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 20(14q24.3) mutation analysis'. These subtypes correlate to 'Time to Death'.
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2 subtypes identified in current cancer cohort by 'Del Peak 21(15q21.3) 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 22(17q25.3) 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 23(18p11.32) 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 24(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 25(19q13.42) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
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2 subtypes identified in current cancer cohort by 'Del Peak 26(22q13.31) 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 27(Xp22.31) 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 28(Xq21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
Statistical Tests | logrank test | t-test | Fisher's exact test | t-test | Fisher's exact test | Fisher's exact test |
Amp Peak 1(1q32 1) |
0.0615 (1.00) |
0.000116 (0.0288) |
0.378 (1.00) |
0.0855 (1.00) |
0.182 (1.00) |
0.377 (1.00) |
Amp Peak 2(4q12) |
0.953 (1.00) |
0.606 (1.00) |
0.748 (1.00) |
0.325 (1.00) |
0.0461 (1.00) |
0.748 (1.00) |
Amp Peak 3(7p11 2) |
0.00366 (0.868) |
0.000626 (0.153) |
0.109 (1.00) |
0.604 (1.00) |
0.0547 (1.00) |
0.34 (1.00) |
Amp Peak 4(7q32 3) |
0.247 (1.00) |
8.46e-05 (0.0212) |
0.0283 (1.00) |
0.844 (1.00) |
0.384 (1.00) |
0.0416 (1.00) |
Amp Peak 5(8q24 21) |
0.903 (1.00) |
0.56 (1.00) |
0.0837 (1.00) |
0.332 (1.00) |
0.011 (1.00) |
0.119 (1.00) |
Amp Peak 6(10p15 1) |
0.739 (1.00) |
0.00528 (1.00) |
0.127 (1.00) |
0.636 (1.00) |
0.00415 (0.976) |
0.255 (1.00) |
Amp Peak 7(10q11 21) |
0.782 (1.00) |
0.692 (1.00) |
0.636 (1.00) |
0.0125 (1.00) |
1 (1.00) |
|
Amp Peak 8(11q23 3) |
0.605 (1.00) |
0.0473 (1.00) |
0.349 (1.00) |
0.568 (1.00) |
0.35 (1.00) |
0.266 (1.00) |
Amp Peak 9(12p13 32) |
0.899 (1.00) |
0.0809 (1.00) |
0.176 (1.00) |
0.47 (1.00) |
0.486 (1.00) |
0.848 (1.00) |
Amp Peak 10(12p11 22) |
0.906 (1.00) |
0.193 (1.00) |
0.0521 (1.00) |
0.448 (1.00) |
0.297 (1.00) |
0.631 (1.00) |
Amp Peak 11(12q14 1) |
1.49e-05 (0.00378) |
0.0516 (1.00) |
0.564 (1.00) |
0.466 (1.00) |
0.117 (1.00) |
0.568 (1.00) |
Amp Peak 12(19p13 3) |
0.828 (1.00) |
0.0993 (1.00) |
0.869 (1.00) |
0.338 (1.00) |
0.0146 (1.00) |
0.744 (1.00) |
Amp Peak 13(19q13 2) |
6.78e-05 (0.0171) |
0.00011 (0.0274) |
0.792 (1.00) |
0.508 (1.00) |
0.396 (1.00) |
0.593 (1.00) |
Amp Peak 14(Xp22 33) |
0.579 (1.00) |
0.877 (1.00) |
1 (1.00) |
0.611 (1.00) |
0.00384 (0.905) |
0.407 (1.00) |
Amp Peak 15(Xq11 2) |
0.666 (1.00) |
0.451 (1.00) |
0.163 (1.00) |
0.687 (1.00) |
0.00489 (1.00) |
0.424 (1.00) |
Del Peak 1(1p36 31) |
0.93 (1.00) |
0.00114 (0.276) |
0.474 (1.00) |
0.85 (1.00) |
7.71e-13 (1.97e-10) |
0.00432 (1.00) |
Del Peak 2(1p32 3) |
0.139 (1.00) |
0.0029 (0.691) |
0.771 (1.00) |
0.952 (1.00) |
7.56e-15 (1.94e-12) |
0.000489 (0.12) |
Del Peak 3(1q43) |
0.942 (1.00) |
0.546 (1.00) |
0.369 (1.00) |
0.244 (1.00) |
0.491 (1.00) |
0.768 (1.00) |
Del Peak 4(2q37 3) |
0.818 (1.00) |
0.0889 (1.00) |
1 (1.00) |
0.542 (1.00) |
0.114 (1.00) |
0.242 (1.00) |
Del Peak 5(3p21 1) |
0.288 (1.00) |
0.0149 (1.00) |
0.634 (1.00) |
0.674 (1.00) |
0.362 (1.00) |
0.147 (1.00) |
Del Peak 6(3q29) |
0.381 (1.00) |
0.655 (1.00) |
0.1 (1.00) |
0.0446 (1.00) |
0.159 (1.00) |
0.481 (1.00) |
Del Peak 7(4q33) |
0.614 (1.00) |
0.813 (1.00) |
0.164 (1.00) |
0.532 (1.00) |
0.133 (1.00) |
0.284 (1.00) |
Del Peak 8(4q35 2) |
0.56 (1.00) |
0.759 (1.00) |
0.125 (1.00) |
0.663 (1.00) |
0.0924 (1.00) |
0.361 (1.00) |
Del Peak 9(5q35 2) |
0.0993 (1.00) |
0.34 (1.00) |
0.305 (1.00) |
0.31 (1.00) |
0.11 (1.00) |
0.0376 (1.00) |
Del Peak 10(6p24 1) |
0.0458 (1.00) |
0.525 (1.00) |
0.31 (1.00) |
0.698 (1.00) |
0.00129 (0.31) |
0.127 (1.00) |
Del Peak 11(6q24 3) |
0.0186 (1.00) |
0.482 (1.00) |
0.43 (1.00) |
0.56 (1.00) |
0.0243 (1.00) |
0.0026 (0.62) |
Del Peak 12(8p23 2) |
0.362 (1.00) |
0.514 (1.00) |
1 (1.00) |
0.249 (1.00) |
0.133 (1.00) |
0.332 (1.00) |
Del Peak 13(9p21 3) |
3.01e-05 (0.00761) |
0.000488 (0.12) |
1 (1.00) |
0.367 (1.00) |
0.0451 (1.00) |
0.000267 (0.0659) |
Del Peak 14(10q26 2) |
0.000151 (0.0374) |
0.0104 (1.00) |
0.0717 (1.00) |
0.33 (1.00) |
0.0167 (1.00) |
0.765 (1.00) |
Del Peak 15(11p15 5) |
0.381 (1.00) |
0.0493 (1.00) |
0.0598 (1.00) |
0.671 (1.00) |
0.00928 (1.00) |
0.304 (1.00) |
Del Peak 16(11q25) |
0.0051 (1.00) |
0.944 (1.00) |
0.246 (1.00) |
0.864 (1.00) |
0.623 (1.00) |
0.568 (1.00) |
Del Peak 17(12q24 11) |
0.861 (1.00) |
0.286 (1.00) |
0.305 (1.00) |
0.34 (1.00) |
0.11 (1.00) |
0.681 (1.00) |
Del Peak 18(13q14 2) |
0.462 (1.00) |
0.853 (1.00) |
0.648 (1.00) |
0.0725 (1.00) |
0.0745 (1.00) |
0.095 (1.00) |
Del Peak 19(13q34) |
0.361 (1.00) |
0.528 (1.00) |
0.506 (1.00) |
0.433 (1.00) |
0.551 (1.00) |
0.138 (1.00) |
Del Peak 20(14q24 3) |
0.000981 (0.238) |
0.184 (1.00) |
0.0455 (1.00) |
0.994 (1.00) |
0.0652 (1.00) |
0.411 (1.00) |
Del Peak 21(15q21 3) |
0.15 (1.00) |
0.34 (1.00) |
1 (1.00) |
0.212 (1.00) |
0.646 (1.00) |
0.681 (1.00) |
Del Peak 22(17q25 3) |
0.606 (1.00) |
0.454 (1.00) |
0.761 (1.00) |
0.731 (1.00) |
1 (1.00) |
1 (1.00) |
Del Peak 23(18p11 32) |
0.822 (1.00) |
0.852 (1.00) |
0.225 (1.00) |
0.349 (1.00) |
0.875 (1.00) |
0.0439 (1.00) |
Del Peak 24(18q23) |
0.722 (1.00) |
0.383 (1.00) |
0.699 (1.00) |
0.843 (1.00) |
0.876 (1.00) |
0.0826 (1.00) |
Del Peak 25(19q13 42) |
0.0266 (1.00) |
0.629 (1.00) |
0.888 (1.00) |
0.566 (1.00) |
9.51e-08 (2.42e-05) |
0.889 (1.00) |
Del Peak 26(22q13 31) |
0.116 (1.00) |
0.281 (1.00) |
0.319 (1.00) |
0.733 (1.00) |
0.0023 (0.552) |
1 (1.00) |
Del Peak 27(Xp22 31) |
0.54 (1.00) |
0.489 (1.00) |
0.319 (1.00) |
0.675 (1.00) |
0.831 (1.00) |
0.411 (1.00) |
Del Peak 28(Xq21 1) |
0.582 (1.00) |
0.233 (1.00) |
0.55 (1.00) |
0.957 (1.00) |
0.206 (1.00) |
0.844 (1.00) |
Cluster Labels | AMP PEAK 1(1Q32.1) MUTATED | AMP PEAK 1(1Q32.1) WILD-TYPE |
---|---|---|
Number of samples | 23 | 184 |
P value = 0.000116 (t-test), Q value = 0.029
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 207 | 43.1 (13.4) |
AMP PEAK 1(1Q32.1) MUTATED | 23 | 53.2 (11.4) |
AMP PEAK 1(1Q32.1) WILD-TYPE | 184 | 41.8 (13.1) |
Cluster Labels | AMP PEAK 2(4Q12) MUTATED | AMP PEAK 2(4Q12) WILD-TYPE |
---|---|---|
Number of samples | 10 | 197 |
Cluster Labels | AMP PEAK 3(7P11.2) MUTATED | AMP PEAK 3(7P11.2) WILD-TYPE |
---|---|---|
Number of samples | 53 | 154 |
P value = 0.000626 (t-test), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 207 | 43.1 (13.4) |
AMP PEAK 3(7P11.2) MUTATED | 53 | 48.7 (13.4) |
AMP PEAK 3(7P11.2) WILD-TYPE | 154 | 41.2 (12.9) |
Cluster Labels | AMP PEAK 4(7Q32.3) MUTATED | AMP PEAK 4(7Q32.3) WILD-TYPE |
---|---|---|
Number of samples | 73 | 134 |
P value = 8.46e-05 (t-test), Q value = 0.021
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 207 | 43.1 (13.4) |
AMP PEAK 4(7Q32.3) MUTATED | 73 | 48.1 (13.1) |
AMP PEAK 4(7Q32.3) WILD-TYPE | 134 | 40.4 (12.9) |
Cluster Labels | AMP PEAK 5(8Q24.21) MUTATED | AMP PEAK 5(8Q24.21) WILD-TYPE |
---|---|---|
Number of samples | 42 | 165 |
Cluster Labels | AMP PEAK 6(10P15.1) MUTATED | AMP PEAK 6(10P15.1) WILD-TYPE |
---|---|---|
Number of samples | 33 | 174 |
Cluster Labels | AMP PEAK 7(10Q11.21) MUTATED | AMP PEAK 7(10Q11.21) WILD-TYPE |
---|---|---|
Number of samples | 4 | 203 |
Cluster Labels | AMP PEAK 8(11Q23.3) MUTATED | AMP PEAK 8(11Q23.3) WILD-TYPE |
---|---|---|
Number of samples | 35 | 172 |
Cluster Labels | AMP PEAK 9(12P13.32) MUTATED | AMP PEAK 9(12P13.32) WILD-TYPE |
---|---|---|
Number of samples | 32 | 175 |
Cluster Labels | AMP PEAK 10(12P11.22) MUTATED | AMP PEAK 10(12P11.22) WILD-TYPE |
---|---|---|
Number of samples | 19 | 188 |
Cluster Labels | AMP PEAK 11(12Q14.1) MUTATED | AMP PEAK 11(12Q14.1) WILD-TYPE |
---|---|---|
Number of samples | 13 | 194 |
P value = 1.49e-05 (logrank test), Q value = 0.0038
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 51 | 0.0 - 211.2 (13.4) |
AMP PEAK 11(12Q14.1) MUTATED | 13 | 9 | 1.2 - 80.0 (12.4) |
AMP PEAK 11(12Q14.1) WILD-TYPE | 193 | 42 | 0.0 - 211.2 (13.4) |
Cluster Labels | AMP PEAK 12(19P13.3) MUTATED | AMP PEAK 12(19P13.3) WILD-TYPE |
---|---|---|
Number of samples | 48 | 159 |
Cluster Labels | AMP PEAK 13(19Q13.2) MUTATED | AMP PEAK 13(19Q13.2) WILD-TYPE |
---|---|---|
Number of samples | 15 | 192 |
P value = 6.78e-05 (logrank test), Q value = 0.017
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 51 | 0.0 - 211.2 (13.4) |
AMP PEAK 13(19Q13.2) MUTATED | 15 | 6 | 0.0 - 43.9 (10.6) |
AMP PEAK 13(19Q13.2) WILD-TYPE | 191 | 45 | 0.1 - 211.2 (14.3) |
P value = 0.00011 (t-test), Q value = 0.027
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 207 | 43.1 (13.4) |
AMP PEAK 13(19Q13.2) MUTATED | 15 | 53.1 (8.0) |
AMP PEAK 13(19Q13.2) WILD-TYPE | 192 | 42.3 (13.5) |
Cluster Labels | AMP PEAK 14(XP22.33) MUTATED | AMP PEAK 14(XP22.33) WILD-TYPE |
---|---|---|
Number of samples | 14 | 193 |
Cluster Labels | AMP PEAK 15(XQ11.2) MUTATED | AMP PEAK 15(XQ11.2) WILD-TYPE |
---|---|---|
Number of samples | 29 | 178 |
Cluster Labels | DEL PEAK 1(1P36.31) MUTATED | DEL PEAK 1(1P36.31) WILD-TYPE |
---|---|---|
Number of samples | 80 | 127 |
P value = 7.71e-13 (Fisher's exact test), Q value = 2e-10
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 63 | 54 | 89 |
DEL PEAK 1(1P36.31) MUTATED | 9 | 11 | 60 |
DEL PEAK 1(1P36.31) WILD-TYPE | 54 | 43 | 29 |
Cluster Labels | DEL PEAK 2(1P32.3) MUTATED | DEL PEAK 2(1P32.3) WILD-TYPE |
---|---|---|
Number of samples | 74 | 133 |
P value = 7.56e-15 (Fisher's exact test), Q value = 1.9e-12
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 63 | 54 | 89 |
DEL PEAK 2(1P32.3) MUTATED | 7 | 8 | 59 |
DEL PEAK 2(1P32.3) WILD-TYPE | 56 | 46 | 30 |
P value = 0.000489 (Fisher's exact test), Q value = 0.12
nPatients | NO | YES |
---|---|---|
ALL | 104 | 103 |
DEL PEAK 2(1P32.3) MUTATED | 25 | 49 |
DEL PEAK 2(1P32.3) WILD-TYPE | 79 | 54 |
Cluster Labels | DEL PEAK 3(1Q43) MUTATED | DEL PEAK 3(1Q43) WILD-TYPE |
---|---|---|
Number of samples | 12 | 195 |
Cluster Labels | DEL PEAK 4(2Q37.3) MUTATED | DEL PEAK 4(2Q37.3) WILD-TYPE |
---|---|---|
Number of samples | 31 | 176 |
Cluster Labels | DEL PEAK 5(3P21.1) MUTATED | DEL PEAK 5(3P21.1) WILD-TYPE |
---|---|---|
Number of samples | 19 | 188 |
Cluster Labels | DEL PEAK 6(3Q29) MUTATED | DEL PEAK 6(3Q29) WILD-TYPE |
---|---|---|
Number of samples | 20 | 187 |
Cluster Labels | DEL PEAK 7(4Q33) MUTATED | DEL PEAK 7(4Q33) WILD-TYPE |
---|---|---|
Number of samples | 60 | 147 |
Cluster Labels | DEL PEAK 8(4Q35.2) MUTATED | DEL PEAK 8(4Q35.2) WILD-TYPE |
---|---|---|
Number of samples | 61 | 146 |
Cluster Labels | DEL PEAK 9(5Q35.2) MUTATED | DEL PEAK 9(5Q35.2) WILD-TYPE |
---|---|---|
Number of samples | 27 | 180 |
Cluster Labels | DEL PEAK 10(6P24.1) MUTATED | DEL PEAK 10(6P24.1) WILD-TYPE |
---|---|---|
Number of samples | 17 | 190 |
Cluster Labels | DEL PEAK 11(6Q24.3) MUTATED | DEL PEAK 11(6Q24.3) WILD-TYPE |
---|---|---|
Number of samples | 30 | 177 |
Cluster Labels | DEL PEAK 12(8P23.2) MUTATED | DEL PEAK 12(8P23.2) WILD-TYPE |
---|---|---|
Number of samples | 10 | 197 |
Cluster Labels | DEL PEAK 13(9P21.3) MUTATED | DEL PEAK 13(9P21.3) WILD-TYPE |
---|---|---|
Number of samples | 74 | 133 |
P value = 3.01e-05 (logrank test), Q value = 0.0076
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 51 | 0.0 - 211.2 (13.4) |
DEL PEAK 13(9P21.3) MUTATED | 73 | 26 | 0.1 - 117.4 (14.7) |
DEL PEAK 13(9P21.3) WILD-TYPE | 133 | 25 | 0.0 - 211.2 (13.4) |
P value = 0.000488 (t-test), Q value = 0.12
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 207 | 43.1 (13.4) |
DEL PEAK 13(9P21.3) MUTATED | 74 | 47.5 (13.2) |
DEL PEAK 13(9P21.3) WILD-TYPE | 133 | 40.7 (13.0) |
P value = 0.000267 (Fisher's exact test), Q value = 0.066
nPatients | NO | YES |
---|---|---|
ALL | 104 | 103 |
DEL PEAK 13(9P21.3) MUTATED | 50 | 24 |
DEL PEAK 13(9P21.3) WILD-TYPE | 54 | 79 |
Cluster Labels | DEL PEAK 14(10Q26.2) MUTATED | DEL PEAK 14(10Q26.2) WILD-TYPE |
---|---|---|
Number of samples | 65 | 142 |
P value = 0.000151 (logrank test), Q value = 0.037
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 51 | 0.0 - 211.2 (13.4) |
DEL PEAK 14(10Q26.2) MUTATED | 65 | 29 | 0.1 - 156.2 (12.4) |
DEL PEAK 14(10Q26.2) WILD-TYPE | 141 | 22 | 0.0 - 211.2 (14.3) |
Cluster Labels | DEL PEAK 15(11P15.5) MUTATED | DEL PEAK 15(11P15.5) WILD-TYPE |
---|---|---|
Number of samples | 43 | 164 |
Cluster Labels | DEL PEAK 16(11Q25) MUTATED | DEL PEAK 16(11Q25) WILD-TYPE |
---|---|---|
Number of samples | 13 | 194 |
Cluster Labels | DEL PEAK 17(12Q24.11) MUTATED | DEL PEAK 17(12Q24.11) WILD-TYPE |
---|---|---|
Number of samples | 27 | 180 |
Cluster Labels | DEL PEAK 18(13Q14.2) MUTATED | DEL PEAK 18(13Q14.2) WILD-TYPE |
---|---|---|
Number of samples | 62 | 145 |
Cluster Labels | DEL PEAK 19(13Q34) MUTATED | DEL PEAK 19(13Q34) WILD-TYPE |
---|---|---|
Number of samples | 48 | 159 |
Cluster Labels | DEL PEAK 20(14Q24.3) MUTATED | DEL PEAK 20(14Q24.3) WILD-TYPE |
---|---|---|
Number of samples | 48 | 159 |
P value = 0.000981 (logrank test), Q value = 0.24
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 206 | 51 | 0.0 - 211.2 (13.4) |
DEL PEAK 20(14Q24.3) MUTATED | 48 | 22 | 0.2 - 130.8 (17.4) |
DEL PEAK 20(14Q24.3) WILD-TYPE | 158 | 29 | 0.0 - 211.2 (12.4) |
Cluster Labels | DEL PEAK 21(15Q21.3) MUTATED | DEL PEAK 21(15Q21.3) WILD-TYPE |
---|---|---|
Number of samples | 26 | 181 |
Cluster Labels | DEL PEAK 22(17Q25.3) MUTATED | DEL PEAK 22(17Q25.3) WILD-TYPE |
---|---|---|
Number of samples | 11 | 196 |
Cluster Labels | DEL PEAK 23(18P11.32) MUTATED | DEL PEAK 23(18P11.32) WILD-TYPE |
---|---|---|
Number of samples | 29 | 178 |
Cluster Labels | DEL PEAK 24(18Q23) MUTATED | DEL PEAK 24(18Q23) WILD-TYPE |
---|---|---|
Number of samples | 32 | 175 |
Cluster Labels | DEL PEAK 25(19Q13.42) MUTATED | DEL PEAK 25(19Q13.42) WILD-TYPE |
---|---|---|
Number of samples | 111 | 96 |
P value = 9.51e-08 (Fisher's exact test), Q value = 2.4e-05
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 63 | 54 | 89 |
DEL PEAK 25(19Q13.42) MUTATED | 20 | 23 | 67 |
DEL PEAK 25(19Q13.42) WILD-TYPE | 43 | 31 | 22 |
Cluster Labels | DEL PEAK 26(22Q13.31) MUTATED | DEL PEAK 26(22Q13.31) WILD-TYPE |
---|---|---|
Number of samples | 29 | 178 |
Cluster Labels | DEL PEAK 27(XP22.31) MUTATED | DEL PEAK 27(XP22.31) WILD-TYPE |
---|---|---|
Number of samples | 48 | 159 |
Cluster Labels | DEL PEAK 28(XQ21.1) MUTATED | DEL PEAK 28(XQ21.1) WILD-TYPE |
---|---|---|
Number of samples | 29 | 178 |
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Cluster data file = all_lesions.conf_99.cnv.cluster.txt
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Clinical data file = LGG-TP.clin.merged.picked.txt
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Number of patients = 207
-
Number of clustering approaches = 43
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Number of selected clinical features = 6
-
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 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.