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 3 clinical features across 146 patients, 2 significant findings detected with Q value < 0.25.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 1(1q21.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 2(3q26.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 3(7p15.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 4(8p11.22) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 5(8q21.13) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 6(10q21.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 7(12q24.32) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 8(14q21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 10(Xp22.11) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 11(Xp21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 12(Xq21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 13(Xq21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 14(Xq21.31) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 15(Xq25) mutation analysis'. These subtypes correlate to 'AGE'.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 16(Xq25) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Amp Peak 17(Xq27.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 1(1p31.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 2(1p21.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 3(1q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 4(1q42.13) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 5(2q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 6(2q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 7(3p13) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 8(3q29) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 9(4q28.1) mutation analysis'. These subtypes correlate to 'AGE'.
-
2 subtypes identified in current cancer cohort by 'Del Peak 10(5q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 11(5q21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 12(6q15) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 13(7q36.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 14(8p21.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
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(10q23.31) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 17(11q23.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 18(12p13.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 19(13q14.13) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 20(16q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 21(16q24.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 22(17p13.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 23(17q21.31) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 24(18q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 25(18q23) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 26(21q22.2) mutation analysis'. These subtypes do not correlate to any clinical features.
-
2 subtypes identified in current cancer cohort by 'Del Peak 27(21q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
Clinical Features |
Time to Death |
AGE |
RADIATIONS RADIATION REGIMENINDICATION |
Statistical Tests | logrank test | t-test | Fisher's exact test |
Amp Peak 1(1q21 3) |
1 (1.00) |
0.835 (1.00) |
1 (1.00) |
Amp Peak 2(3q26 2) |
1 (1.00) |
0.128 (1.00) |
1 (1.00) |
Amp Peak 3(7p15 3) |
1 (1.00) |
0.454 (1.00) |
0.258 (1.00) |
Amp Peak 4(8p11 22) |
1 (1.00) |
0.379 (1.00) |
1 (1.00) |
Amp Peak 5(8q21 13) |
1 (1.00) |
0.0354 (1.00) |
0.33 (1.00) |
Amp Peak 6(10q21 2) |
1 (1.00) |
0.215 (1.00) |
1 (1.00) |
Amp Peak 7(12q24 32) |
1 (1.00) |
0.988 (1.00) |
0.221 (1.00) |
Amp Peak 8(14q21 1) |
1 (1.00) |
0.0144 (1.00) |
0.192 (1.00) |
Amp Peak 10(Xp22 11) |
1 (1.00) |
0.25 (1.00) |
1 (1.00) |
Amp Peak 11(Xp21 1) |
1 (1.00) |
0.125 (1.00) |
1 (1.00) |
Amp Peak 12(Xq21 1) |
1 (1.00) |
0.731 (1.00) |
1 (1.00) |
Amp Peak 13(Xq21 1) |
1 (1.00) |
0.334 (1.00) |
1 (1.00) |
Amp Peak 14(Xq21 31) |
1 (1.00) |
0.235 (1.00) |
1 (1.00) |
Amp Peak 15(Xq25) |
1 (1.00) |
7.25e-09 (9.36e-07) |
1 (1.00) |
Amp Peak 16(Xq25) |
1 (1.00) |
0.724 (1.00) |
1 (1.00) |
Amp Peak 17(Xq27 1) |
1 (1.00) |
0.295 (1.00) |
1 (1.00) |
Del Peak 1(1p31 3) |
1 (1.00) |
0.787 (1.00) |
1 (1.00) |
Del Peak 2(1p21 3) |
1 (1.00) |
0.998 (1.00) |
1 (1.00) |
Del Peak 3(1q23 1) |
1 (1.00) |
0.643 (1.00) |
1 (1.00) |
Del Peak 4(1q42 13) |
1 (1.00) |
0.156 (1.00) |
1 (1.00) |
Del Peak 5(2q22 1) |
1 (1.00) |
0.0945 (1.00) |
1 (1.00) |
Del Peak 6(2q22 3) |
1 (1.00) |
0.149 (1.00) |
1 (1.00) |
Del Peak 7(3p13) |
1 (1.00) |
0.319 (1.00) |
0.0396 (1.00) |
Del Peak 8(3q29) |
1 (1.00) |
0.347 (1.00) |
1 (1.00) |
Del Peak 9(4q28 1) |
1 (1.00) |
0.000488 (0.0624) |
1 (1.00) |
Del Peak 10(5q11 2) |
1 (1.00) |
0.0689 (1.00) |
1 (1.00) |
Del Peak 11(5q21 1) |
1 (1.00) |
0.0196 (1.00) |
0.586 (1.00) |
Del Peak 12(6q15) |
1 (1.00) |
0.0337 (1.00) |
0.168 (1.00) |
Del Peak 13(7q36 1) |
1 (1.00) |
0.0663 (1.00) |
1 (1.00) |
Del Peak 14(8p21 3) |
1 (1.00) |
0.231 (1.00) |
1 (1.00) |
Del Peak 15(8p11 21) |
1 (1.00) |
0.0851 (1.00) |
0.176 (1.00) |
Del Peak 16(10q23 31) |
1 (1.00) |
0.975 (1.00) |
0.653 (1.00) |
Del Peak 17(11q23 2) |
1 (1.00) |
0.635 (1.00) |
1 (1.00) |
Del Peak 18(12p13 2) |
1 (1.00) |
0.768 (1.00) |
1 (1.00) |
Del Peak 19(13q14 13) |
1 (1.00) |
0.00565 (0.717) |
0.184 (1.00) |
Del Peak 20(16q22 3) |
1 (1.00) |
0.0237 (1.00) |
0.324 (1.00) |
Del Peak 21(16q24 1) |
1 (1.00) |
0.123 (1.00) |
1 (1.00) |
Del Peak 22(17p13 1) |
1 (1.00) |
0.447 (1.00) |
1 (1.00) |
Del Peak 23(17q21 31) |
1 (1.00) |
0.675 (1.00) |
1 (1.00) |
Del Peak 24(18q22 1) |
1 (1.00) |
0.659 (1.00) |
1 (1.00) |
Del Peak 25(18q23) |
1 (1.00) |
0.0888 (1.00) |
0.631 (1.00) |
Del Peak 26(21q22 2) |
1 (1.00) |
0.858 (1.00) |
0.331 (1.00) |
Del Peak 27(21q22 3) |
1 (1.00) |
0.689 (1.00) |
0.18 (1.00) |
Cluster Labels | AMP PEAK 1(1Q21.3) MUTATED | AMP PEAK 1(1Q21.3) WILD-TYPE |
---|---|---|
Number of samples | 9 | 137 |
Cluster Labels | AMP PEAK 2(3Q26.2) MUTATED | AMP PEAK 2(3Q26.2) WILD-TYPE |
---|---|---|
Number of samples | 23 | 123 |
Cluster Labels | AMP PEAK 3(7P15.3) MUTATED | AMP PEAK 3(7P15.3) WILD-TYPE |
---|---|---|
Number of samples | 29 | 117 |
Cluster Labels | AMP PEAK 4(8P11.22) MUTATED | AMP PEAK 4(8P11.22) WILD-TYPE |
---|---|---|
Number of samples | 15 | 131 |
Cluster Labels | AMP PEAK 5(8Q21.13) MUTATED | AMP PEAK 5(8Q21.13) WILD-TYPE |
---|---|---|
Number of samples | 37 | 109 |
Cluster Labels | AMP PEAK 6(10Q21.2) MUTATED | AMP PEAK 6(10Q21.2) WILD-TYPE |
---|---|---|
Number of samples | 7 | 139 |
Cluster Labels | AMP PEAK 7(12Q24.32) MUTATED | AMP PEAK 7(12Q24.32) WILD-TYPE |
---|---|---|
Number of samples | 7 | 139 |
Cluster Labels | AMP PEAK 8(14Q21.1) MUTATED | AMP PEAK 8(14Q21.1) WILD-TYPE |
---|---|---|
Number of samples | 6 | 140 |
Cluster Labels | AMP PEAK 10(XP22.11) MUTATED | AMP PEAK 10(XP22.11) WILD-TYPE |
---|---|---|
Number of samples | 4 | 142 |
Cluster Labels | AMP PEAK 11(XP21.1) MUTATED | AMP PEAK 11(XP21.1) WILD-TYPE |
---|---|---|
Number of samples | 4 | 142 |
Cluster Labels | AMP PEAK 12(XQ21.1) MUTATED | AMP PEAK 12(XQ21.1) WILD-TYPE |
---|---|---|
Number of samples | 7 | 139 |
Cluster Labels | AMP PEAK 13(XQ21.1) MUTATED | AMP PEAK 13(XQ21.1) WILD-TYPE |
---|---|---|
Number of samples | 5 | 141 |
Cluster Labels | AMP PEAK 14(XQ21.31) MUTATED | AMP PEAK 14(XQ21.31) WILD-TYPE |
---|---|---|
Number of samples | 5 | 141 |
Cluster Labels | AMP PEAK 15(XQ25) MUTATED | AMP PEAK 15(XQ25) WILD-TYPE |
---|---|---|
Number of samples | 3 | 143 |
P value = 7.25e-09 (t-test), Q value = 9.4e-07
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 146 | 60.4 (7.0) |
AMP PEAK 15(XQ25) MUTATED | 3 | 65.7 (0.6) |
AMP PEAK 15(XQ25) WILD-TYPE | 143 | 60.3 (7.0) |
Cluster Labels | AMP PEAK 16(XQ25) MUTATED | AMP PEAK 16(XQ25) WILD-TYPE |
---|---|---|
Number of samples | 6 | 140 |
Cluster Labels | AMP PEAK 17(XQ27.1) MUTATED | AMP PEAK 17(XQ27.1) WILD-TYPE |
---|---|---|
Number of samples | 9 | 137 |
Cluster Labels | DEL PEAK 1(1P31.3) MUTATED | DEL PEAK 1(1P31.3) WILD-TYPE |
---|---|---|
Number of samples | 19 | 127 |
Cluster Labels | DEL PEAK 2(1P21.3) MUTATED | DEL PEAK 2(1P21.3) WILD-TYPE |
---|---|---|
Number of samples | 13 | 133 |
Cluster Labels | DEL PEAK 3(1Q23.1) MUTATED | DEL PEAK 3(1Q23.1) WILD-TYPE |
---|---|---|
Number of samples | 5 | 141 |
Cluster Labels | DEL PEAK 4(1Q42.13) MUTATED | DEL PEAK 4(1Q42.13) WILD-TYPE |
---|---|---|
Number of samples | 14 | 132 |
Cluster Labels | DEL PEAK 5(2Q22.1) MUTATED | DEL PEAK 5(2Q22.1) WILD-TYPE |
---|---|---|
Number of samples | 19 | 127 |
Cluster Labels | DEL PEAK 6(2Q22.3) MUTATED | DEL PEAK 6(2Q22.3) WILD-TYPE |
---|---|---|
Number of samples | 18 | 128 |
Cluster Labels | DEL PEAK 7(3P13) MUTATED | DEL PEAK 7(3P13) WILD-TYPE |
---|---|---|
Number of samples | 26 | 120 |
Cluster Labels | DEL PEAK 8(3Q29) MUTATED | DEL PEAK 8(3Q29) WILD-TYPE |
---|---|---|
Number of samples | 9 | 137 |
Cluster Labels | DEL PEAK 9(4Q28.1) MUTATED | DEL PEAK 9(4Q28.1) WILD-TYPE |
---|---|---|
Number of samples | 11 | 135 |
P value = 0.000488 (t-test), Q value = 0.062
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 146 | 60.4 (7.0) |
DEL PEAK 9(4Q28.1) MUTATED | 11 | 65.5 (3.7) |
DEL PEAK 9(4Q28.1) WILD-TYPE | 135 | 60.0 (7.0) |
Cluster Labels | DEL PEAK 10(5Q11.2) MUTATED | DEL PEAK 10(5Q11.2) WILD-TYPE |
---|---|---|
Number of samples | 23 | 123 |
Cluster Labels | DEL PEAK 11(5Q21.1) MUTATED | DEL PEAK 11(5Q21.1) WILD-TYPE |
---|---|---|
Number of samples | 26 | 120 |
Cluster Labels | DEL PEAK 12(6Q15) MUTATED | DEL PEAK 12(6Q15) WILD-TYPE |
---|---|---|
Number of samples | 49 | 97 |
Cluster Labels | DEL PEAK 13(7Q36.1) MUTATED | DEL PEAK 13(7Q36.1) WILD-TYPE |
---|---|---|
Number of samples | 5 | 141 |
Cluster Labels | DEL PEAK 14(8P21.3) MUTATED | DEL PEAK 14(8P21.3) WILD-TYPE |
---|---|---|
Number of samples | 87 | 59 |
Cluster Labels | DEL PEAK 15(8P11.21) MUTATED | DEL PEAK 15(8P11.21) WILD-TYPE |
---|---|---|
Number of samples | 47 | 99 |
Cluster Labels | DEL PEAK 16(10Q23.31) MUTATED | DEL PEAK 16(10Q23.31) WILD-TYPE |
---|---|---|
Number of samples | 53 | 93 |
Cluster Labels | DEL PEAK 17(11Q23.2) MUTATED | DEL PEAK 17(11Q23.2) WILD-TYPE |
---|---|---|
Number of samples | 16 | 130 |
Cluster Labels | DEL PEAK 18(12P13.2) MUTATED | DEL PEAK 18(12P13.2) WILD-TYPE |
---|---|---|
Number of samples | 31 | 115 |
Cluster Labels | DEL PEAK 19(13Q14.13) MUTATED | DEL PEAK 19(13Q14.13) WILD-TYPE |
---|---|---|
Number of samples | 68 | 78 |
Cluster Labels | DEL PEAK 20(16Q22.3) MUTATED | DEL PEAK 20(16Q22.3) WILD-TYPE |
---|---|---|
Number of samples | 45 | 101 |
Cluster Labels | DEL PEAK 21(16Q24.1) MUTATED | DEL PEAK 21(16Q24.1) WILD-TYPE |
---|---|---|
Number of samples | 58 | 88 |
Cluster Labels | DEL PEAK 22(17P13.1) MUTATED | DEL PEAK 22(17P13.1) WILD-TYPE |
---|---|---|
Number of samples | 39 | 107 |
Cluster Labels | DEL PEAK 23(17Q21.31) MUTATED | DEL PEAK 23(17Q21.31) WILD-TYPE |
---|---|---|
Number of samples | 26 | 120 |
Cluster Labels | DEL PEAK 24(18Q22.1) MUTATED | DEL PEAK 24(18Q22.1) WILD-TYPE |
---|---|---|
Number of samples | 37 | 109 |
Cluster Labels | DEL PEAK 25(18Q23) MUTATED | DEL PEAK 25(18Q23) WILD-TYPE |
---|---|---|
Number of samples | 43 | 103 |
Cluster Labels | DEL PEAK 26(21Q22.2) MUTATED | DEL PEAK 26(21Q22.2) WILD-TYPE |
---|---|---|
Number of samples | 48 | 98 |
Cluster Labels | DEL PEAK 27(21Q22.3) MUTATED | DEL PEAK 27(21Q22.3) WILD-TYPE |
---|---|---|
Number of samples | 46 | 100 |
-
Cluster data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = PRAD-TP.clin.merged.picked.txt
-
Number of patients = 146
-
Number of clustering approaches = 43
-
Number of selected clinical features = 3
-
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.