This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 44 focal events and 12 clinical features across 52 patients, no significant finding detected with Q value < 0.25.
-
No focal cnvs related to clinical features.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
NUMBERPACKYEARSSMOKED | YEAROFTOBACCOSMOKINGONSET |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
||
nCNV (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test | t-test | Fisher's exact test | t-test | |
AMP PEAK 1(1P34 2) MUTATION ANALYSIS | 3 (6%) | 49 |
0.159 (1.00) |
0.947 (1.00) |
1 (1.00) |
1 (1.00) |
0.193 (1.00) |
0.59 (1.00) |
0.271 (1.00) |
0.0604 (1.00) |
0.0112 (1.00) |
|||
AMP PEAK 2(1P12) MUTATION ANALYSIS | 6 (12%) | 46 |
0.574 (1.00) |
0.909 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.612 (1.00) |
0.284 (1.00) |
0.674 (1.00) |
1 (1.00) |
0.52 (1.00) |
0.241 (1.00) |
||
AMP PEAK 3(7Q22 1) MUTATION ANALYSIS | 13 (25%) | 39 |
0.456 (1.00) |
0.799 (1.00) |
0.712 (1.00) |
1 (1.00) |
1 (1.00) |
0.249 (1.00) |
0.541 (1.00) |
1 (1.00) |
0.0604 (1.00) |
0.619 (1.00) |
||
AMP PEAK 4(8Q24 21) MUTATION ANALYSIS | 19 (37%) | 33 |
0.09 (1.00) |
0.971 (1.00) |
0.733 (1.00) |
0.641 (1.00) |
1 (1.00) |
0.341 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.0344 (1.00) |
0.51 (1.00) |
0.385 (1.00) |
0.241 (1.00) |
AMP PEAK 5(9P13 3) MUTATION ANALYSIS | 5 (10%) | 47 |
0.0756 (1.00) |
0.847 (1.00) |
0.105 (1.00) |
1 (1.00) |
0.325 (1.00) |
0.16 (1.00) |
0.652 (1.00) |
1 (1.00) |
0.706 (1.00) |
0.845 (1.00) |
||
AMP PEAK 6(11P11 2) MUTATION ANALYSIS | 4 (8%) | 48 |
0.967 (1.00) |
0.327 (1.00) |
0.93 (1.00) |
1 (1.00) |
1 (1.00) |
0.247 (1.00) |
1 (1.00) |
1 (1.00) |
0.614 (1.00) |
0.456 (1.00) |
||
AMP PEAK 7(12P13 33) MUTATION ANALYSIS | 7 (13%) | 45 |
0.259 (1.00) |
0.842 (1.00) |
0.502 (1.00) |
0.53 (1.00) |
1 (1.00) |
1 (1.00) |
0.0396 (1.00) |
0.48 (1.00) |
0.267 (1.00) |
0.67 (1.00) |
||
AMP PEAK 8(12P11 21) MUTATION ANALYSIS | 10 (19%) | 42 |
0.253 (1.00) |
0.218 (1.00) |
0.428 (1.00) |
1 (1.00) |
1 (1.00) |
0.361 (1.00) |
0.0313 (1.00) |
0.336 (1.00) |
0.0234 (1.00) |
0.741 (1.00) |
||
AMP PEAK 9(12Q15) MUTATION ANALYSIS | 6 (12%) | 46 |
0.249 (1.00) |
0.306 (1.00) |
0.777 (1.00) |
1 (1.00) |
0.316 (1.00) |
0.527 (1.00) |
0.0836 (1.00) |
0.0993 (1.00) |
0.0461 (1.00) |
0.465 (1.00) |
||
AMP PEAK 10(17P11 2) MUTATION ANALYSIS | 3 (6%) | 49 |
0.0626 (1.00) |
0.947 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.358 (1.00) |
||||
AMP PEAK 11(17Q21 33) MUTATION ANALYSIS | 7 (13%) | 45 |
0.483 (1.00) |
0.231 (1.00) |
0.657 (1.00) |
1 (1.00) |
0.656 (1.00) |
0.574 (1.00) |
0.69 (1.00) |
1 (1.00) |
1 (1.00) |
0.658 (1.00) |
||
AMP PEAK 12(18Q11 2) MUTATION ANALYSIS | 14 (27%) | 38 |
0.489 (1.00) |
0.848 (1.00) |
0.169 (1.00) |
0.307 (1.00) |
0.475 (1.00) |
0.00325 (1.00) |
1 (1.00) |
1 (1.00) |
0.461 (1.00) |
0.415 (1.00) |
0.0298 (1.00) |
0.682 (1.00) |
AMP PEAK 13(19Q13 13) MUTATION ANALYSIS | 10 (19%) | 42 |
0.912 (1.00) |
0.982 (1.00) |
0.738 (1.00) |
0.569 (1.00) |
1 (1.00) |
0.828 (1.00) |
0.157 (1.00) |
0.655 (1.00) |
0.711 (1.00) |
0.382 (1.00) |
1 (1.00) |
0.816 (1.00) |
AMP PEAK 14(20Q13 2) MUTATION ANALYSIS | 13 (25%) | 39 |
0.204 (1.00) |
0.551 (1.00) |
0.353 (1.00) |
1 (1.00) |
0.253 (1.00) |
0.859 (1.00) |
0.106 (1.00) |
0.419 (1.00) |
0.349 (1.00) |
0.0825 (1.00) |
||
AMP PEAK 15(XP22 11) MUTATION ANALYSIS | 4 (8%) | 48 |
0.899 (1.00) |
0.426 (1.00) |
0.902 (1.00) |
1 (1.00) |
0.562 (1.00) |
1 (1.00) |
0.0393 (1.00) |
0.347 (1.00) |
0.688 (1.00) |
0.731 (1.00) |
||
AMP PEAK 16(XQ27 1) MUTATION ANALYSIS | 6 (12%) | 46 |
0.94 (1.00) |
0.905 (1.00) |
0.472 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.397 (1.00) |
0.416 (1.00) |
0.149 (1.00) |
0.911 (1.00) |
||
DEL PEAK 1(1P36 22) MUTATION ANALYSIS | 9 (17%) | 43 |
0.196 (1.00) |
0.0547 (1.00) |
0.496 (1.00) |
1 (1.00) |
0.666 (1.00) |
0.26 (1.00) |
0.0637 (1.00) |
0.638 (1.00) |
0.282 (1.00) |
0.155 (1.00) |
0.333 (1.00) |
0.173 (1.00) |
DEL PEAK 2(1P36 11) MUTATION ANALYSIS | 12 (23%) | 40 |
0.21 (1.00) |
0.275 (1.00) |
0.703 (1.00) |
1 (1.00) |
0.709 (1.00) |
0.184 (1.00) |
0.0449 (1.00) |
1 (1.00) |
0.282 (1.00) |
0.155 (1.00) |
0.604 (1.00) |
0.435 (1.00) |
DEL PEAK 3(1P21 2) MUTATION ANALYSIS | 9 (17%) | 43 |
0.451 (1.00) |
0.518 (1.00) |
0.496 (1.00) |
1 (1.00) |
0.666 (1.00) |
0.26 (1.00) |
0.0637 (1.00) |
0.638 (1.00) |
0.282 (1.00) |
0.155 (1.00) |
0.146 (1.00) |
0.258 (1.00) |
DEL PEAK 4(5Q14 2) MUTATION ANALYSIS | 9 (17%) | 43 |
0.735 (1.00) |
0.588 (1.00) |
0.842 (1.00) |
0.573 (1.00) |
0.666 (1.00) |
1 (1.00) |
0.716 (1.00) |
0.638 (1.00) |
0.379 (1.00) |
0.523 (1.00) |
||
DEL PEAK 5(5Q15) MUTATION ANALYSIS | 10 (19%) | 42 |
0.735 (1.00) |
0.376 (1.00) |
0.789 (1.00) |
0.569 (1.00) |
0.42 (1.00) |
1 (1.00) |
0.483 (1.00) |
1 (1.00) |
0.333 (1.00) |
0.505 (1.00) |
||
DEL PEAK 6(6P25 2) MUTATION ANALYSIS | 19 (37%) | 33 |
0.0984 (1.00) |
0.497 (1.00) |
0.687 (1.00) |
0.641 (1.00) |
0.739 (1.00) |
0.0425 (1.00) |
0.253 (1.00) |
0.749 (1.00) |
0.953 (1.00) |
0.704 (1.00) |
0.887 (1.00) |
0.608 (1.00) |
DEL PEAK 7(6P22 3) MUTATION ANALYSIS | 19 (37%) | 33 |
0.372 (1.00) |
0.566 (1.00) |
0.687 (1.00) |
0.641 (1.00) |
0.739 (1.00) |
0.167 (1.00) |
0.0856 (1.00) |
0.749 (1.00) |
0.852 (1.00) |
0.704 (1.00) |
1 (1.00) |
0.67 (1.00) |
DEL PEAK 8(6Q22 33) MUTATION ANALYSIS | 24 (46%) | 28 |
0.177 (1.00) |
0.843 (1.00) |
0.53 (1.00) |
0.358 (1.00) |
1 (1.00) |
0.0435 (1.00) |
0.781 (1.00) |
1 (1.00) |
0.537 (1.00) |
0.789 (1.00) |
0.779 (1.00) |
0.541 (1.00) |
DEL PEAK 9(7Q36 1) MUTATION ANALYSIS | 5 (10%) | 47 |
0.734 (1.00) |
0.771 (1.00) |
0.408 (1.00) |
0.41 (1.00) |
1 (1.00) |
1 (1.00) |
0.652 (1.00) |
1 (1.00) |
1 (1.00) |
0.881 (1.00) |
||
DEL PEAK 10(8P21 3) MUTATION ANALYSIS | 15 (29%) | 37 |
0.212 (1.00) |
0.241 (1.00) |
0.362 (1.00) |
1 (1.00) |
0.47 (1.00) |
0.479 (1.00) |
0.234 (1.00) |
0.5 (1.00) |
0.282 (1.00) |
0.0138 (1.00) |
0.457 (1.00) |
|
DEL PEAK 11(8Q12 1) MUTATION ANALYSIS | 4 (8%) | 48 |
0.567 (1.00) |
0.352 (1.00) |
0.302 (1.00) |
1 (1.00) |
1 (1.00) |
0.122 (1.00) |
1 (1.00) |
0.347 (1.00) |
0.404 (1.00) |
0.616 (1.00) |
||
DEL PEAK 12(9P21 3) MUTATION ANALYSIS | 29 (56%) | 23 |
0.55 (1.00) |
0.879 (1.00) |
0.214 (1.00) |
0.644 (1.00) |
0.329 (1.00) |
0.173 (1.00) |
0.785 (1.00) |
0.788 (1.00) |
0.233 (1.00) |
0.521 (1.00) |
0.00132 (0.634) |
0.306 (1.00) |
DEL PEAK 13(10Q23 2) MUTATION ANALYSIS | 10 (19%) | 42 |
0.253 (1.00) |
0.206 (1.00) |
0.738 (1.00) |
1 (1.00) |
1 (1.00) |
0.137 (1.00) |
0.483 (1.00) |
1 (1.00) |
0.152 (1.00) |
0.422 (1.00) |
0.348 (1.00) |
|
DEL PEAK 14(11P15 4) MUTATION ANALYSIS | 10 (19%) | 42 |
0.119 (1.00) |
0.876 (1.00) |
0.789 (1.00) |
0.569 (1.00) |
0.42 (1.00) |
0.0327 (1.00) |
1 (1.00) |
0.655 (1.00) |
0.436 (1.00) |
0.773 (1.00) |
0.639 (1.00) |
0.272 (1.00) |
DEL PEAK 15(12P12 3) MUTATION ANALYSIS | 8 (15%) | 44 |
0.0294 (1.00) |
0.71 (1.00) |
0.709 (1.00) |
1 (1.00) |
1 (1.00) |
0.373 (1.00) |
0.123 (1.00) |
0.538 (1.00) |
0.0635 (1.00) |
0.189 (1.00) |
||
DEL PEAK 16(12Q12) MUTATION ANALYSIS | 7 (13%) | 45 |
0.0275 (1.00) |
0.929 (1.00) |
0.354 (1.00) |
0.53 (1.00) |
0.331 (1.00) |
0.0134 (1.00) |
1 (1.00) |
1 (1.00) |
0.599 (1.00) |
0.755 (1.00) |
0.198 (1.00) |
|
DEL PEAK 17(12Q24 31) MUTATION ANALYSIS | 12 (23%) | 40 |
0.902 (1.00) |
0.99 (1.00) |
0.703 (1.00) |
1 (1.00) |
1 (1.00) |
0.144 (1.00) |
1 (1.00) |
1 (1.00) |
0.932 (1.00) |
0.752 (1.00) |
0.349 (1.00) |
0.0714 (1.00) |
DEL PEAK 18(15Q15 1) MUTATION ANALYSIS | 9 (17%) | 43 |
0.614 (1.00) |
0.217 (1.00) |
0.566 (1.00) |
1 (1.00) |
1 (1.00) |
0.338 (1.00) |
0.272 (1.00) |
0.638 (1.00) |
0.379 (1.00) |
0.461 (1.00) |
||
DEL PEAK 19(17P11 2) MUTATION ANALYSIS | 19 (37%) | 33 |
0.106 (1.00) |
0.741 (1.00) |
0.31 (1.00) |
0.145 (1.00) |
1 (1.00) |
0.194 (1.00) |
0.568 (1.00) |
0.749 (1.00) |
0.0459 (1.00) |
0.208 (1.00) |
0.00477 (1.00) |
0.578 (1.00) |
DEL PEAK 20(17Q22) MUTATION ANALYSIS | 15 (29%) | 37 |
0.404 (1.00) |
0.596 (1.00) |
0.16 (1.00) |
0.305 (1.00) |
0.47 (1.00) |
0.0538 (1.00) |
1 (1.00) |
1 (1.00) |
0.202 (1.00) |
0.208 (1.00) |
0.00415 (1.00) |
0.873 (1.00) |
DEL PEAK 21(18P11 32) MUTATION ANALYSIS | 17 (33%) | 35 |
0.622 (1.00) |
0.00357 (1.00) |
0.772 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.732 (1.00) |
0.668 (1.00) |
0.236 (1.00) |
0.481 (1.00) |
0.803 (1.00) |
DEL PEAK 22(18Q12 1) MUTATION ANALYSIS | 27 (52%) | 25 |
0.456 (1.00) |
0.863 (1.00) |
0.544 (1.00) |
0.662 (1.00) |
1 (1.00) |
0.886 (1.00) |
0.788 (1.00) |
0.61 (1.00) |
0.622 (1.00) |
0.0631 (1.00) |
0.138 (1.00) |
0.519 (1.00) |
DEL PEAK 23(18Q21 2) MUTATION ANALYSIS | 33 (63%) | 19 |
0.669 (1.00) |
0.301 (1.00) |
0.261 (1.00) |
0.342 (1.00) |
0.317 (1.00) |
0.295 (1.00) |
0.775 (1.00) |
0.551 (1.00) |
0.917 (1.00) |
0.00406 (1.00) |
0.402 (1.00) |
|
DEL PEAK 24(19Q13 33) MUTATION ANALYSIS | 5 (10%) | 47 |
0.399 (1.00) |
0.769 (1.00) |
0.844 (1.00) |
1 (1.00) |
0.578 (1.00) |
1 (1.00) |
0.652 (1.00) |
1 (1.00) |
0.242 (1.00) |
0.529 (1.00) |
||
DEL PEAK 25(21Q22 11) MUTATION ANALYSIS | 16 (31%) | 36 |
0.291 (1.00) |
0.418 (1.00) |
0.0625 (1.00) |
0.308 (1.00) |
0.0776 (1.00) |
0.0377 (1.00) |
0.229 (1.00) |
0.514 (1.00) |
0.609 (1.00) |
0.81 (1.00) |
0.189 (1.00) |
0.0824 (1.00) |
DEL PEAK 26(21Q22 11) MUTATION ANALYSIS | 16 (31%) | 36 |
0.291 (1.00) |
0.418 (1.00) |
0.0625 (1.00) |
0.308 (1.00) |
0.0776 (1.00) |
0.0377 (1.00) |
0.229 (1.00) |
0.514 (1.00) |
0.609 (1.00) |
0.81 (1.00) |
0.189 (1.00) |
0.0824 (1.00) |
DEL PEAK 27(22Q13 31) MUTATION ANALYSIS | 12 (23%) | 40 |
0.261 (1.00) |
0.552 (1.00) |
0.126 (1.00) |
0.578 (1.00) |
0.709 (1.00) |
0.0102 (1.00) |
0.186 (1.00) |
0.658 (1.00) |
0.00809 (1.00) |
0.711 (1.00) |
0.0185 (1.00) |
0.234 (1.00) |
DEL PEAK 28(XQ21 1) MUTATION ANALYSIS | 6 (12%) | 46 |
0.732 (1.00) |
0.848 (1.00) |
0.777 (1.00) |
1 (1.00) |
0.316 (1.00) |
0.375 (1.00) |
0.397 (1.00) |
0.416 (1.00) |
0.281 (1.00) |
0.665 (1.00) |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = PAAD-TP.clin.merged.picked.txt
-
Number of patients = 52
-
Number of significantly focal cnvs = 44
-
Number of selected clinical features = 12
-
Exclude genes that fewer than K tumors have mutations, 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 tumors with and without gene mutations using 't.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 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.