This pipeline computes the correlation between significant copy number variation (cnv) genes and selected clinical features.
Testing the association between copy number variation of 29 peak regions and 9 clinical features across 490 patients, 25 significant findings detected with Q value < 0.25.
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Amp Peak 3(3q26.32) cnvs correlated to 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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Amp Peak 7(8q24.22) cnvs correlated to 'PATHOLOGY.T'.
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Del Peak 8(3q11.2) cnvs correlated to 'GENDER'.
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Del Peak 9(4q34.3) cnvs correlated to 'Time to Death', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
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Del Peak 13(9p23) cnvs correlated to 'Time to Death', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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Del Peak 14(9p21.3) cnvs correlated to 'Time to Death', 'GENDER', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
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Del Peak 15(10q23.31) cnvs correlated to 'PATHOLOGY.T'.
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Del Peak 16(13q13.3) cnvs correlated to 'Time to Death', 'PATHOLOGY.T', and 'TUMOR.STAGE'.
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Del Peak 17(14q31.1) cnvs correlated to 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
PATHOLOGY T |
PATHOLOGY N |
PATHOLOGICSPREAD(M) |
TUMOR STAGE |
NEOADJUVANT THERAPY |
||
nCNV (%) | nWild-Type | 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 | Fisher's exact test | |
Del Peak 14(9p21 3) | 152 (31%) | 338 |
2.41e-06 (0.000611) |
0.0321 (1.00) |
0.00102 (0.241) |
0.656 (1.00) |
1.39e-07 (3.55e-05) |
0.0596 (1.00) |
7.19e-05 (0.0176) |
4.76e-08 (1.23e-05) |
0.648 (1.00) |
Del Peak 13(9p23) | 144 (29%) | 346 |
0.000157 (0.0381) |
0.0169 (1.00) |
0.00349 (0.793) |
0.656 (1.00) |
1.86e-05 (0.00462) |
0.262 (1.00) |
0.000908 (0.215) |
7.69e-06 (0.00194) |
0.634 (1.00) |
Del Peak 17(14q31 1) | 218 (44%) | 272 |
0.00205 (0.472) |
0.0697 (1.00) |
0.342 (1.00) |
0.0872 (1.00) |
0.000171 (0.0413) |
0.000119 (0.029) |
0.00106 (0.249) |
3.97e-05 (0.00981) |
0.177 (1.00) |
Amp Peak 3(3q26 32) | 78 (16%) | 412 |
0.142 (1.00) |
0.662 (1.00) |
0.365 (1.00) |
0.152 (1.00) |
3.86e-05 (0.00958) |
0.0569 (1.00) |
5.27e-05 (0.013) |
8.48e-06 (0.00213) |
0.181 (1.00) |
Del Peak 9(4q34 3) | 76 (16%) | 414 |
0.000608 (0.145) |
0.604 (1.00) |
0.432 (1.00) |
0.0261 (1.00) |
4.49e-07 (0.000115) |
1 (1.00) |
0.00879 (1.00) |
3.13e-06 (0.000792) |
0.571 (1.00) |
Del Peak 16(13q13 3) | 76 (16%) | 414 |
0.000925 (0.218) |
0.923 (1.00) |
0.794 (1.00) |
0.748 (1.00) |
1.5e-05 (0.00375) |
0.49 (1.00) |
0.0387 (1.00) |
0.00037 (0.0892) |
1 (1.00) |
Amp Peak 7(8q24 22) | 72 (15%) | 418 |
0.0314 (1.00) |
0.0131 (1.00) |
0.11 (1.00) |
0.297 (1.00) |
0.000684 (0.163) |
0.734 (1.00) |
0.0514 (1.00) |
0.00159 (0.368) |
1 (1.00) |
Del Peak 8(3q11 2) | 150 (31%) | 340 |
0.658 (1.00) |
0.0137 (1.00) |
1.18e-07 (3.04e-05) |
0.749 (1.00) |
0.13 (1.00) |
0.787 (1.00) |
0.59 (1.00) |
0.454 (1.00) |
1 (1.00) |
Del Peak 15(10q23 31) | 90 (18%) | 400 |
0.227 (1.00) |
0.232 (1.00) |
0.0271 (1.00) |
0.764 (1.00) |
0.000545 (0.131) |
1 (1.00) |
0.335 (1.00) |
0.0207 (1.00) |
0.59 (1.00) |
Amp Peak 1(1q24 1) | 60 (12%) | 430 |
0.207 (1.00) |
0.177 (1.00) |
0.665 (1.00) |
0.499 (1.00) |
0.164 (1.00) |
0.0762 (1.00) |
0.34 (1.00) |
0.321 (1.00) |
0.481 (1.00) |
Amp Peak 2(1q32 1) | 59 (12%) | 431 |
0.448 (1.00) |
0.0798 (1.00) |
0.771 (1.00) |
0.499 (1.00) |
0.176 (1.00) |
0.71 (1.00) |
0.704 (1.00) |
0.257 (1.00) |
0.475 (1.00) |
Amp Peak 4(4q32 1) | 14 (3%) | 476 |
0.0605 (1.00) |
0.404 (1.00) |
0.26 (1.00) |
0.411 (1.00) |
0.242 (1.00) |
0.576 (1.00) |
0.464 (1.00) |
0.417 (1.00) |
1 (1.00) |
Amp Peak 5(5q35 1) | 309 (63%) | 181 |
0.0406 (1.00) |
0.0714 (1.00) |
0.141 (1.00) |
0.944 (1.00) |
0.292 (1.00) |
0.311 (1.00) |
0.305 (1.00) |
0.624 (1.00) |
0.656 (1.00) |
Amp Peak 6(7q36 3) | 162 (33%) | 328 |
0.648 (1.00) |
0.766 (1.00) |
0.0349 (1.00) |
0.57 (1.00) |
0.0553 (1.00) |
0.442 (1.00) |
0.0052 (1.00) |
0.0196 (1.00) |
0.338 (1.00) |
Amp Peak 8(10p14) | 15 (3%) | 475 |
0.0834 (1.00) |
0.156 (1.00) |
0.592 (1.00) |
0.887 (1.00) |
0.00579 (1.00) |
0.161 (1.00) |
0.267 (1.00) |
0.0276 (1.00) |
0.145 (1.00) |
Amp Peak 9(17q24 3) | 37 (8%) | 453 |
0.0536 (1.00) |
0.0714 (1.00) |
0.858 (1.00) |
0.471 (1.00) |
0.501 (1.00) |
0.361 (1.00) |
0.243 (1.00) |
0.868 (1.00) |
0.326 (1.00) |
Amp Peak 10(Xp22 2) | 34 (7%) | 456 |
0.319 (1.00) |
0.847 (1.00) |
0.711 (1.00) |
0.726 (1.00) |
0.0555 (1.00) |
0.658 (1.00) |
0.0831 (1.00) |
0.00651 (1.00) |
0.041 (1.00) |
Amp Peak 11(Xp11 4) | 35 (7%) | 455 |
0.576 (1.00) |
0.887 (1.00) |
0.854 (1.00) |
0.726 (1.00) |
0.0448 (1.00) |
0.658 (1.00) |
0.0478 (1.00) |
0.00315 (0.718) |
0.0433 (1.00) |
Del Peak 1(1p36 23) | 97 (20%) | 393 |
0.0336 (1.00) |
0.0962 (1.00) |
0.122 (1.00) |
0.284 (1.00) |
0.104 (1.00) |
1 (1.00) |
0.0836 (1.00) |
0.157 (1.00) |
0.0554 (1.00) |
Del Peak 2(1p31 1) | 72 (15%) | 418 |
0.228 (1.00) |
0.0813 (1.00) |
0.0157 (1.00) |
0.284 (1.00) |
0.0532 (1.00) |
0.723 (1.00) |
0.377 (1.00) |
0.183 (1.00) |
0.158 (1.00) |
Del Peak 3(1q43) | 38 (8%) | 452 |
0.693 (1.00) |
0.354 (1.00) |
1 (1.00) |
0.0661 (1.00) |
0.374 (1.00) |
1 (1.00) |
0.751 (1.00) |
1 (1.00) |
|
Del Peak 4(2q37 3) | 48 (10%) | 442 |
0.661 (1.00) |
0.658 (1.00) |
0.152 (1.00) |
0.849 (1.00) |
1 (1.00) |
0.402 (1.00) |
0.552 (1.00) |
1 (1.00) |
|
Del Peak 5(3p25 3) | 430 (88%) | 60 |
0.7 (1.00) |
0.848 (1.00) |
0.665 (1.00) |
0.0817 (1.00) |
0.00145 (0.339) |
1 (1.00) |
0.707 (1.00) |
0.0136 (1.00) |
0.481 (1.00) |
Del Peak 6(3p24 3) | 431 (88%) | 59 |
0.494 (1.00) |
0.879 (1.00) |
0.56 (1.00) |
0.0817 (1.00) |
0.00159 (0.368) |
1 (1.00) |
0.848 (1.00) |
0.0152 (1.00) |
0.475 (1.00) |
Del Peak 7(3p12 2) | 282 (58%) | 208 |
0.563 (1.00) |
0.77 (1.00) |
0.00211 (0.484) |
0.741 (1.00) |
0.211 (1.00) |
0.627 (1.00) |
0.529 (1.00) |
0.228 (1.00) |
0.655 (1.00) |
Del Peak 10(6q26) | 142 (29%) | 348 |
0.54 (1.00) |
0.324 (1.00) |
0.00905 (1.00) |
0.256 (1.00) |
0.669 (1.00) |
0.0198 (1.00) |
0.412 (1.00) |
0.353 (1.00) |
0.63 (1.00) |
Del Peak 11(6q26) | 142 (29%) | 348 |
0.563 (1.00) |
0.257 (1.00) |
0.00478 (1.00) |
0.256 (1.00) |
0.669 (1.00) |
0.0198 (1.00) |
0.412 (1.00) |
0.353 (1.00) |
1 (1.00) |
Del Peak 12(8p23 2) | 145 (30%) | 345 |
0.0279 (1.00) |
0.121 (1.00) |
0.255 (1.00) |
0.893 (1.00) |
0.169 (1.00) |
0.786 (1.00) |
0.0548 (1.00) |
0.135 (1.00) |
1 (1.00) |
Del Peak 18(Xq23) | 55 (11%) | 435 |
0.296 (1.00) |
0.704 (1.00) |
0.232 (1.00) |
0.309 (1.00) |
0.658 (1.00) |
0.17 (1.00) |
0.141 (1.00) |
0.0991 (1.00) |
P value = 3.86e-05 (Fisher's exact test), Q value = 0.0096
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 239 | 64 | 176 | 11 |
AMP PEAK 3(3Q26.32) MUTATED | 22 | 8 | 44 | 4 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 217 | 56 | 132 | 7 |
P value = 5.27e-05 (Fisher's exact test), Q value = 0.013
nPatients | M0 | M1 |
---|---|---|
ALL | 414 | 76 |
AMP PEAK 3(3Q26.32) MUTATED | 53 | 25 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 361 | 51 |
P value = 8.48e-06 (Fisher's exact test), Q value = 0.0021
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 235 | 52 | 123 | 80 |
AMP PEAK 3(3Q26.32) MUTATED | 21 | 6 | 25 | 26 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 214 | 46 | 98 | 54 |
P value = 0.000684 (Fisher's exact test), Q value = 0.16
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 239 | 64 | 176 | 11 |
AMP PEAK 7(8Q24.22) MUTATED | 20 | 11 | 39 | 2 |
AMP PEAK 7(8Q24.22) WILD-TYPE | 219 | 53 | 137 | 9 |
P value = 1.18e-07 (Fisher's exact test), Q value = 3e-05
nPatients | FEMALE | MALE |
---|---|---|
ALL | 319 | 171 |
DEL PEAK 8(3Q11.2) MUTATED | 123 | 27 |
DEL PEAK 8(3Q11.2) WILD-TYPE | 196 | 144 |
P value = 0.000608 (logrank test), Q value = 0.15
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 487 | 157 | 0.1 - 111.0 (34.6) |
DEL PEAK 9(4Q34.3) MUTATED | 76 | 38 | 0.2 - 91.4 (35.1) |
DEL PEAK 9(4Q34.3) WILD-TYPE | 411 | 119 | 0.1 - 111.0 (34.3) |
P value = 4.49e-07 (Fisher's exact test), Q value = 0.00011
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 239 | 64 | 176 | 11 |
DEL PEAK 9(4Q34.3) MUTATED | 19 | 8 | 43 | 6 |
DEL PEAK 9(4Q34.3) WILD-TYPE | 220 | 56 | 133 | 5 |
P value = 3.13e-06 (Fisher's exact test), Q value = 0.00079
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 235 | 52 | 123 | 80 |
DEL PEAK 9(4Q34.3) MUTATED | 18 | 6 | 30 | 22 |
DEL PEAK 9(4Q34.3) WILD-TYPE | 217 | 46 | 93 | 58 |
P value = 0.000157 (logrank test), Q value = 0.038
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 487 | 157 | 0.1 - 111.0 (34.6) |
DEL PEAK 13(9P23) MUTATED | 143 | 65 | 0.2 - 109.9 (36.1) |
DEL PEAK 13(9P23) WILD-TYPE | 344 | 92 | 0.1 - 111.0 (34.3) |
P value = 1.86e-05 (Fisher's exact test), Q value = 0.0046
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 239 | 64 | 176 | 11 |
DEL PEAK 13(9P23) MUTATED | 50 | 15 | 74 | 5 |
DEL PEAK 13(9P23) WILD-TYPE | 189 | 49 | 102 | 6 |
P value = 0.000908 (Fisher's exact test), Q value = 0.22
nPatients | M0 | M1 |
---|---|---|
ALL | 414 | 76 |
DEL PEAK 13(9P23) MUTATED | 109 | 35 |
DEL PEAK 13(9P23) WILD-TYPE | 305 | 41 |
P value = 7.69e-06 (Fisher's exact test), Q value = 0.0019
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 235 | 52 | 123 | 80 |
DEL PEAK 13(9P23) MUTATED | 48 | 11 | 49 | 36 |
DEL PEAK 13(9P23) WILD-TYPE | 187 | 41 | 74 | 44 |
P value = 2.41e-06 (logrank test), Q value = 0.00061
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 487 | 157 | 0.1 - 111.0 (34.6) |
DEL PEAK 14(9P21.3) MUTATED | 152 | 72 | 0.2 - 109.9 (31.5) |
DEL PEAK 14(9P21.3) WILD-TYPE | 335 | 85 | 0.1 - 111.0 (35.5) |
P value = 0.00102 (Fisher's exact test), Q value = 0.24
nPatients | FEMALE | MALE |
---|---|---|
ALL | 319 | 171 |
DEL PEAK 14(9P21.3) MUTATED | 115 | 37 |
DEL PEAK 14(9P21.3) WILD-TYPE | 204 | 134 |
P value = 1.39e-07 (Fisher's exact test), Q value = 3.5e-05
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 239 | 64 | 176 | 11 |
DEL PEAK 14(9P21.3) MUTATED | 51 | 14 | 81 | 6 |
DEL PEAK 14(9P21.3) WILD-TYPE | 188 | 50 | 95 | 5 |
P value = 7.19e-05 (Fisher's exact test), Q value = 0.018
nPatients | M0 | M1 |
---|---|---|
ALL | 414 | 76 |
DEL PEAK 14(9P21.3) MUTATED | 113 | 39 |
DEL PEAK 14(9P21.3) WILD-TYPE | 301 | 37 |
P value = 4.76e-08 (Fisher's exact test), Q value = 1.2e-05
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 235 | 52 | 123 | 80 |
DEL PEAK 14(9P21.3) MUTATED | 49 | 10 | 52 | 41 |
DEL PEAK 14(9P21.3) WILD-TYPE | 186 | 42 | 71 | 39 |
P value = 0.000545 (Fisher's exact test), Q value = 0.13
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 239 | 64 | 176 | 11 |
DEL PEAK 15(10Q23.31) MUTATED | 31 | 10 | 43 | 6 |
DEL PEAK 15(10Q23.31) WILD-TYPE | 208 | 54 | 133 | 5 |
P value = 0.000925 (logrank test), Q value = 0.22
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 487 | 157 | 0.1 - 111.0 (34.6) |
DEL PEAK 16(13Q13.3) MUTATED | 75 | 34 | 0.1 - 89.4 (28.5) |
DEL PEAK 16(13Q13.3) WILD-TYPE | 412 | 123 | 0.1 - 111.0 (36.1) |
P value = 1.5e-05 (Fisher's exact test), Q value = 0.0038
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 239 | 64 | 176 | 11 |
DEL PEAK 16(13Q13.3) MUTATED | 28 | 3 | 39 | 6 |
DEL PEAK 16(13Q13.3) WILD-TYPE | 211 | 61 | 137 | 5 |
P value = 0.00037 (Fisher's exact test), Q value = 0.089
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 235 | 52 | 123 | 80 |
DEL PEAK 16(13Q13.3) MUTATED | 27 | 2 | 27 | 20 |
DEL PEAK 16(13Q13.3) WILD-TYPE | 208 | 50 | 96 | 60 |
P value = 0.000171 (Fisher's exact test), Q value = 0.041
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 239 | 64 | 176 | 11 |
DEL PEAK 17(14Q31.1) MUTATED | 83 | 35 | 96 | 4 |
DEL PEAK 17(14Q31.1) WILD-TYPE | 156 | 29 | 80 | 7 |
P value = 0.000119 (Fisher's exact test), Q value = 0.029
nPatients | 0 | 1 |
---|---|---|
ALL | 227 | 18 |
DEL PEAK 17(14Q31.1) MUTATED | 96 | 16 |
DEL PEAK 17(14Q31.1) WILD-TYPE | 131 | 2 |
P value = 0.00106 (Fisher's exact test), Q value = 0.25
nPatients | M0 | M1 |
---|---|---|
ALL | 414 | 76 |
DEL PEAK 17(14Q31.1) MUTATED | 171 | 47 |
DEL PEAK 17(14Q31.1) WILD-TYPE | 243 | 29 |
P value = 3.97e-05 (Fisher's exact test), Q value = 0.0098
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 235 | 52 | 123 | 80 |
DEL PEAK 17(14Q31.1) MUTATED | 79 | 25 | 68 | 46 |
DEL PEAK 17(14Q31.1) WILD-TYPE | 156 | 27 | 55 | 34 |
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Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
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Clinical data file = KIRC.clin.merged.picked.txt
-
Number of patients = 490
-
Number of copy number variation regions = 29
-
Number of selected clinical features = 9
-
Exclude regions that fewer than K tumors have alterations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs 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 tumors with and without gene cnvs using 't.test' function in R
For binary or multi-class clinical features (nominal or ordinal), 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.