This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between subtypes identified by 22 different clustering approaches and 8 clinical features across 103 patients, 2 significant findings detected with Q value < 0.25.
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2 subtypes identified in current cancer cohort by 'Amp Peak 1(2q32.1) 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 2(3p14.1) 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 3(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 'Amp Peak 4(6p12.3) 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 5(7q22.1) 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 6(17q25.2) 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 7(19p13.2) 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 8(19q13.11) 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 1(1p36.31) 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 2(2p11.2) 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(3p22.1) 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 5(4q31.22) 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(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 7(6q22.31) 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 8(9p21.3) 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 9(14q11.2) 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(14q23.3) 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 11(14q32.2) 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 12(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 'Del Peak 13(Xq21.31) mutation analysis'. These subtypes correlate to 'Time to Death'.
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2 subtypes identified in current cancer cohort by 'Del Peak 14(Xq28) mutation analysis'. These subtypes correlate to 'Time to Death'.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
Statistical Tests | logrank test | t-test | Fisher's exact test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test |
Amp Peak 1(2q32 1) |
0.602 (1.00) |
0.388 (1.00) |
0.793 (1.00) |
0.5 (1.00) |
0.134 (1.00) |
0.508 (1.00) |
0.0518 (1.00) |
0.065 (1.00) |
Amp Peak 2(3p14 1) |
0.601 (1.00) |
0.73 (1.00) |
0.238 (1.00) |
0.141 (1.00) |
0.0823 (1.00) |
1 (1.00) |
0.651 (1.00) |
0.265 (1.00) |
Amp Peak 3(5q35 2) |
0.885 (1.00) |
0.979 (1.00) |
1 (1.00) |
0.395 (1.00) |
0.206 (1.00) |
1 (1.00) |
0.668 (1.00) |
0.337 (1.00) |
Amp Peak 4(6p12 3) |
0.57 (1.00) |
0.349 (1.00) |
1 (1.00) |
0.164 (1.00) |
0.506 (1.00) |
0.217 (1.00) |
0.262 (1.00) |
|
Amp Peak 5(7q22 1) |
0.0626 (1.00) |
0.784 (1.00) |
0.135 (1.00) |
0.2 (1.00) |
0.00703 (1.00) |
0.686 (1.00) |
0.39 (1.00) |
0.00168 (0.276) |
Amp Peak 6(17q25 2) |
0.547 (1.00) |
0.0893 (1.00) |
0.0692 (1.00) |
0.556 (1.00) |
0.356 (1.00) |
0.783 (1.00) |
0.018 (1.00) |
0.704 (1.00) |
Amp Peak 7(19p13 2) |
0.999 (1.00) |
0.0722 (1.00) |
1 (1.00) |
0.144 (1.00) |
0.0769 (1.00) |
1 (1.00) |
1 (1.00) |
0.741 (1.00) |
Amp Peak 8(19q13 11) |
0.374 (1.00) |
0.261 (1.00) |
1 (1.00) |
0.777 (1.00) |
1 (1.00) |
0.715 (1.00) |
0.807 (1.00) |
|
Del Peak 1(1p36 31) |
0.236 (1.00) |
0.636 (1.00) |
0.616 (1.00) |
0.396 (1.00) |
0.125 (1.00) |
0.263 (1.00) |
0.0666 (1.00) |
0.107 (1.00) |
Del Peak 2(2p11 2) |
0.357 (1.00) |
0.716 (1.00) |
1 (1.00) |
0.526 (1.00) |
1 (1.00) |
0.561 (1.00) |
||
Del Peak 3(2q37 3) |
0.652 (1.00) |
0.338 (1.00) |
0.324 (1.00) |
0.00909 (1.00) |
0.32 (1.00) |
0.0239 (1.00) |
||
Del Peak 4(3p22 1) |
0.211 (1.00) |
0.0512 (1.00) |
0.661 (1.00) |
0.0728 (1.00) |
0.55 (1.00) |
0.342 (1.00) |
0.0746 (1.00) |
|
Del Peak 5(4q31 22) |
0.13 (1.00) |
0.281 (1.00) |
0.324 (1.00) |
0.221 (1.00) |
0.359 (1.00) |
0.0927 (1.00) |
0.262 (1.00) |
|
Del Peak 6(5q35 2) |
0.61 (1.00) |
0.113 (1.00) |
0.265 (1.00) |
0.0124 (1.00) |
0.138 (1.00) |
0.307 (1.00) |
0.0445 (1.00) |
|
Del Peak 7(6q22 31) |
0.0444 (1.00) |
0.911 (1.00) |
0.0506 (1.00) |
0.392 (1.00) |
0.0277 (1.00) |
0.836 (1.00) |
0.548 (1.00) |
0.153 (1.00) |
Del Peak 8(9p21 3) |
0.00552 (0.895) |
0.326 (1.00) |
0.0389 (1.00) |
0.424 (1.00) |
0.0033 (0.538) |
0.311 (1.00) |
0.0361 (1.00) |
0.0102 (1.00) |
Del Peak 9(14q11 2) |
0.252 (1.00) |
0.96 (1.00) |
0.802 (1.00) |
0.457 (1.00) |
0.284 (1.00) |
0.663 (1.00) |
0.145 (1.00) |
0.101 (1.00) |
Del Peak 10(14q23 3) |
0.231 (1.00) |
0.326 (1.00) |
0.616 (1.00) |
0.396 (1.00) |
0.197 (1.00) |
0.239 (1.00) |
0.0769 (1.00) |
0.0771 (1.00) |
Del Peak 11(14q32 2) |
0.231 (1.00) |
0.296 (1.00) |
1 (1.00) |
0.396 (1.00) |
0.435 (1.00) |
0.239 (1.00) |
0.0421 (1.00) |
0.0655 (1.00) |
Del Peak 12(19q13 42) |
0.386 (1.00) |
0.617 (1.00) |
1 (1.00) |
0.377 (1.00) |
0.681 (1.00) |
1 (1.00) |
0.408 (1.00) |
|
Del Peak 13(Xq21 31) |
0.000103 (0.017) |
0.209 (1.00) |
0.234 (1.00) |
0.424 (1.00) |
0.0409 (1.00) |
0.312 (1.00) |
0.17 (1.00) |
0.155 (1.00) |
Del Peak 14(Xq28) |
4.26e-05 (0.00707) |
0.282 (1.00) |
0.135 (1.00) |
0.475 (1.00) |
0.3 (1.00) |
0.329 (1.00) |
0.496 (1.00) |
0.337 (1.00) |
Cluster Labels | AMP PEAK 1(2Q32.1) MUTATED | AMP PEAK 1(2Q32.1) WILD-TYPE |
---|---|---|
Number of samples | 20 | 83 |
Cluster Labels | AMP PEAK 2(3P14.1) MUTATED | AMP PEAK 2(3P14.1) WILD-TYPE |
---|---|---|
Number of samples | 27 | 76 |
Cluster Labels | AMP PEAK 3(5Q35.2) MUTATED | AMP PEAK 3(5Q35.2) WILD-TYPE |
---|---|---|
Number of samples | 14 | 89 |
Cluster Labels | AMP PEAK 4(6P12.3) MUTATED | AMP PEAK 4(6P12.3) WILD-TYPE |
---|---|---|
Number of samples | 4 | 99 |
Cluster Labels | AMP PEAK 5(7Q22.1) MUTATED | AMP PEAK 5(7Q22.1) WILD-TYPE |
---|---|---|
Number of samples | 59 | 44 |
Cluster Labels | AMP PEAK 6(17Q25.2) MUTATED | AMP PEAK 6(17Q25.2) WILD-TYPE |
---|---|---|
Number of samples | 70 | 33 |
Cluster Labels | AMP PEAK 7(19P13.2) MUTATED | AMP PEAK 7(19P13.2) WILD-TYPE |
---|---|---|
Number of samples | 13 | 90 |
Cluster Labels | AMP PEAK 8(19Q13.11) MUTATED | AMP PEAK 8(19Q13.11) WILD-TYPE |
---|---|---|
Number of samples | 4 | 99 |
Cluster Labels | DEL PEAK 1(1P36.31) MUTATED | DEL PEAK 1(1P36.31) WILD-TYPE |
---|---|---|
Number of samples | 22 | 81 |
Cluster Labels | DEL PEAK 2(2P11.2) MUTATED | DEL PEAK 2(2P11.2) WILD-TYPE |
---|---|---|
Number of samples | 3 | 100 |
Cluster Labels | DEL PEAK 3(2Q37.3) MUTATED | DEL PEAK 3(2Q37.3) WILD-TYPE |
---|---|---|
Number of samples | 5 | 98 |
Cluster Labels | DEL PEAK 4(3P22.1) MUTATED | DEL PEAK 4(3P22.1) WILD-TYPE |
---|---|---|
Number of samples | 6 | 97 |
Cluster Labels | DEL PEAK 5(4Q31.22) MUTATED | DEL PEAK 5(4Q31.22) WILD-TYPE |
---|---|---|
Number of samples | 11 | 92 |
Cluster Labels | DEL PEAK 6(5Q35.2) MUTATED | DEL PEAK 6(5Q35.2) WILD-TYPE |
---|---|---|
Number of samples | 8 | 95 |
Cluster Labels | DEL PEAK 7(6Q22.31) MUTATED | DEL PEAK 7(6Q22.31) WILD-TYPE |
---|---|---|
Number of samples | 12 | 91 |
Cluster Labels | DEL PEAK 8(9P21.3) MUTATED | DEL PEAK 8(9P21.3) WILD-TYPE |
---|---|---|
Number of samples | 16 | 87 |
Cluster Labels | DEL PEAK 9(14Q11.2) MUTATED | DEL PEAK 9(14Q11.2) WILD-TYPE |
---|---|---|
Number of samples | 23 | 80 |
Cluster Labels | DEL PEAK 10(14Q23.3) MUTATED | DEL PEAK 10(14Q23.3) WILD-TYPE |
---|---|---|
Number of samples | 22 | 81 |
Cluster Labels | DEL PEAK 11(14Q32.2) MUTATED | DEL PEAK 11(14Q32.2) WILD-TYPE |
---|---|---|
Number of samples | 22 | 81 |
Cluster Labels | DEL PEAK 12(19Q13.42) MUTATED | DEL PEAK 12(19Q13.42) WILD-TYPE |
---|---|---|
Number of samples | 8 | 95 |
Cluster Labels | DEL PEAK 13(XQ21.31) MUTATED | DEL PEAK 13(XQ21.31) WILD-TYPE |
---|---|---|
Number of samples | 15 | 88 |
P value = 0.000103 (logrank test), Q value = 0.017
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 96 | 14 | 0.0 - 182.7 (13.7) |
DEL PEAK 13(XQ21.31) MUTATED | 14 | 5 | 0.0 - 79.8 (9.2) |
DEL PEAK 13(XQ21.31) WILD-TYPE | 82 | 9 | 0.0 - 182.7 (15.1) |
Cluster Labels | DEL PEAK 14(XQ28) MUTATED | DEL PEAK 14(XQ28) WILD-TYPE |
---|---|---|
Number of samples | 14 | 89 |
P value = 4.26e-05 (logrank test), Q value = 0.0071
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 96 | 14 | 0.0 - 182.7 (13.7) |
DEL PEAK 14(XQ28) MUTATED | 13 | 4 | 0.0 - 22.9 (9.6) |
DEL PEAK 14(XQ28) WILD-TYPE | 83 | 10 | 0.0 - 182.7 (15.5) |
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Cluster data file = all_lesions.conf_99.cnv.cluster.txt
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Clinical data file = KIRP-TP.clin.merged.picked.txt
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Number of patients = 103
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Number of clustering approaches = 22
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Number of selected clinical features = 8
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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.