This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.
Testing the association between copy number variation 40 focal events and 8 molecular subtypes across 56 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.
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4q cnv correlated to 'MIRSEQ_CNMF'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 40 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, one significant finding detected.
|
Clinical Features |
CN CNMF |
METHLYATION CNMF |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
| nCNV (%) | nWild-Type | Fisher's exact test | Chi-square test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
| 4q | 36 (64%) | 20 |
0.0319 (1.00) |
0.021 (1.00) |
0.0175 (1.00) |
0.0483 (1.00) |
0.000546 (0.175) |
0.116 (1.00) |
0.0577 (1.00) |
0.116 (1.00) |
| 1p | 33 (59%) | 23 |
0.175 (1.00) |
0.612 (1.00) |
0.69 (1.00) |
0.549 (1.00) |
0.496 (1.00) |
0.83 (1.00) |
0.667 (1.00) |
0.444 (1.00) |
| 1q | 40 (71%) | 16 |
0.866 (1.00) |
0.549 (1.00) |
0.767 (1.00) |
0.842 (1.00) |
0.868 (1.00) |
0.604 (1.00) |
0.833 (1.00) |
0.428 (1.00) |
| 2p | 25 (45%) | 31 |
0.606 (1.00) |
0.0432 (1.00) |
0.219 (1.00) |
0.144 (1.00) |
0.364 (1.00) |
0.0479 (1.00) |
0.245 (1.00) |
0.0308 (1.00) |
| 2q | 23 (41%) | 33 |
0.758 (1.00) |
0.0468 (1.00) |
0.116 (1.00) |
0.341 (1.00) |
0.411 (1.00) |
0.0395 (1.00) |
0.312 (1.00) |
0.0293 (1.00) |
| 3p | 32 (57%) | 24 |
0.35 (1.00) |
0.105 (1.00) |
0.335 (1.00) |
0.123 (1.00) |
0.531 (1.00) |
0.765 (1.00) |
0.729 (1.00) |
0.825 (1.00) |
| 3q | 37 (66%) | 19 |
0.693 (1.00) |
0.107 (1.00) |
0.0669 (1.00) |
0.0514 (1.00) |
0.1 (1.00) |
0.0828 (1.00) |
0.302 (1.00) |
0.0817 (1.00) |
| 4p | 40 (71%) | 16 |
0.0507 (1.00) |
0.0815 (1.00) |
0.0577 (1.00) |
0.09 (1.00) |
0.00932 (1.00) |
0.198 (1.00) |
0.246 (1.00) |
0.169 (1.00) |
| 5p | 32 (57%) | 24 |
0.709 (1.00) |
0.913 (1.00) |
0.352 (1.00) |
0.447 (1.00) |
0.862 (1.00) |
0.699 (1.00) |
0.834 (1.00) |
0.366 (1.00) |
| 5q | 26 (46%) | 30 |
0.792 (1.00) |
0.386 (1.00) |
0.791 (1.00) |
0.261 (1.00) |
0.525 (1.00) |
0.327 (1.00) |
0.0666 (1.00) |
0.183 (1.00) |
| 6p | 35 (62%) | 21 |
0.0884 (1.00) |
0.425 (1.00) |
0.886 (1.00) |
0.661 (1.00) |
0.959 (1.00) |
0.298 (1.00) |
0.935 (1.00) |
0.579 (1.00) |
| 6q | 34 (61%) | 22 |
0.0229 (1.00) |
0.248 (1.00) |
0.937 (1.00) |
0.57 (1.00) |
0.866 (1.00) |
1 (1.00) |
0.509 (1.00) |
0.779 (1.00) |
| 7p | 34 (61%) | 22 |
0.248 (1.00) |
0.164 (1.00) |
0.323 (1.00) |
0.165 (1.00) |
0.959 (1.00) |
0.755 (1.00) |
0.935 (1.00) |
0.795 (1.00) |
| 7q | 30 (54%) | 26 |
0.428 (1.00) |
0.553 (1.00) |
0.286 (1.00) |
0.406 (1.00) |
0.924 (1.00) |
0.601 (1.00) |
0.854 (1.00) |
0.513 (1.00) |
| 8p | 42 (75%) | 14 |
0.449 (1.00) |
0.542 (1.00) |
0.094 (1.00) |
0.646 (1.00) |
0.204 (1.00) |
0.723 (1.00) |
0.309 (1.00) |
0.51 (1.00) |
| 8q | 39 (70%) | 17 |
0.116 (1.00) |
0.165 (1.00) |
0.0553 (1.00) |
0.531 (1.00) |
0.251 (1.00) |
0.643 (1.00) |
0.156 (1.00) |
0.457 (1.00) |
| 9p | 40 (71%) | 16 |
0.177 (1.00) |
0.0407 (1.00) |
0.82 (1.00) |
0.849 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.833 (1.00) |
0.641 (1.00) |
| 9q | 41 (73%) | 15 |
0.166 (1.00) |
0.00528 (1.00) |
1 (1.00) |
0.813 (1.00) |
0.636 (1.00) |
1 (1.00) |
0.935 (1.00) |
0.78 (1.00) |
| 10p | 44 (79%) | 12 |
0.91 (1.00) |
0.202 (1.00) |
0.147 (1.00) |
0.413 (1.00) |
0.33 (1.00) |
0.0957 (1.00) |
0.892 (1.00) |
0.165 (1.00) |
| 10q | 38 (68%) | 18 |
1 (1.00) |
0.0116 (1.00) |
0.0439 (1.00) |
0.21 (1.00) |
0.882 (1.00) |
0.333 (1.00) |
0.53 (1.00) |
0.481 (1.00) |
| 11p | 31 (55%) | 25 |
0.837 (1.00) |
0.0912 (1.00) |
0.42 (1.00) |
0.496 (1.00) |
0.329 (1.00) |
0.241 (1.00) |
0.651 (1.00) |
0.3 (1.00) |
| 11q | 31 (55%) | 25 |
0.837 (1.00) |
0.0427 (1.00) |
0.304 (1.00) |
0.145 (1.00) |
0.329 (1.00) |
0.241 (1.00) |
0.568 (1.00) |
0.3 (1.00) |
| 12p | 35 (62%) | 21 |
0.409 (1.00) |
0.129 (1.00) |
0.0174 (1.00) |
0.0306 (1.00) |
0.678 (1.00) |
0.269 (1.00) |
0.418 (1.00) |
0.666 (1.00) |
| 12q | 25 (45%) | 31 |
0.682 (1.00) |
0.947 (1.00) |
0.479 (1.00) |
0.578 (1.00) |
0.934 (1.00) |
0.73 (1.00) |
0.412 (1.00) |
0.455 (1.00) |
| 13q | 41 (73%) | 15 |
0.914 (1.00) |
0.484 (1.00) |
1 (1.00) |
0.622 (1.00) |
0.958 (1.00) |
0.574 (1.00) |
0.967 (1.00) |
1 (1.00) |
| 14q | 34 (61%) | 22 |
0.681 (1.00) |
0.377 (1.00) |
0.628 (1.00) |
0.0768 (1.00) |
0.862 (1.00) |
1 (1.00) |
0.611 (1.00) |
0.671 (1.00) |
| 15q | 36 (64%) | 20 |
0.0212 (1.00) |
0.535 (1.00) |
0.495 (1.00) |
0.54 (1.00) |
1 (1.00) |
1 (1.00) |
0.628 (1.00) |
1 (1.00) |
| 16p | 42 (75%) | 14 |
0.356 (1.00) |
0.298 (1.00) |
0.795 (1.00) |
0.835 (1.00) |
0.645 (1.00) |
0.704 (1.00) |
0.188 (1.00) |
1 (1.00) |
| 16q | 43 (77%) | 13 |
0.649 (1.00) |
0.814 (1.00) |
0.922 (1.00) |
0.831 (1.00) |
0.801 (1.00) |
1 (1.00) |
0.278 (1.00) |
1 (1.00) |
| 17p | 43 (77%) | 13 |
0.742 (1.00) |
0.0782 (1.00) |
0.922 (1.00) |
0.248 (1.00) |
0.892 (1.00) |
0.546 (1.00) |
1 (1.00) |
0.757 (1.00) |
| 17q | 35 (62%) | 21 |
1 (1.00) |
0.104 (1.00) |
0.323 (1.00) |
0.031 (1.00) |
0.222 (1.00) |
0.269 (1.00) |
0.63 (1.00) |
0.666 (1.00) |
| 18p | 36 (64%) | 20 |
0.725 (1.00) |
0.304 (1.00) |
1 (1.00) |
0.308 (1.00) |
0.719 (1.00) |
0.264 (1.00) |
0.932 (1.00) |
0.266 (1.00) |
| 18q | 34 (61%) | 22 |
0.593 (1.00) |
0.819 (1.00) |
0.86 (1.00) |
0.138 (1.00) |
0.319 (1.00) |
0.132 (1.00) |
0.611 (1.00) |
0.147 (1.00) |
| 19p | 39 (70%) | 17 |
0.843 (1.00) |
0.208 (1.00) |
0.806 (1.00) |
0.796 (1.00) |
0.212 (1.00) |
0.756 (1.00) |
0.374 (1.00) |
0.532 (1.00) |
| 19q | 41 (73%) | 15 |
0.392 (1.00) |
0.0702 (1.00) |
0.732 (1.00) |
0.338 (1.00) |
0.0867 (1.00) |
0.723 (1.00) |
0.0687 (1.00) |
0.51 (1.00) |
| 20p | 44 (79%) | 12 |
0.49 (1.00) |
0.73 (1.00) |
0.271 (1.00) |
0.488 (1.00) |
0.801 (1.00) |
0.546 (1.00) |
0.783 (1.00) |
0.757 (1.00) |
| 20q | 48 (86%) | 8 |
0.604 (1.00) |
0.761 (1.00) |
0.0414 (1.00) |
0.394 (1.00) |
0.179 (1.00) |
0.261 (1.00) |
0.148 (1.00) |
0.369 (1.00) |
| 21q | 35 (62%) | 21 |
0.553 (1.00) |
0.574 (1.00) |
0.563 (1.00) |
0.563 (1.00) |
0.854 (1.00) |
0.546 (1.00) |
0.912 (1.00) |
0.308 (1.00) |
| 22q | 41 (73%) | 15 |
0.793 (1.00) |
0.883 (1.00) |
0.384 (1.00) |
0.501 (1.00) |
0.795 (1.00) |
0.574 (1.00) |
0.596 (1.00) |
0.524 (1.00) |
| xq | 33 (59%) | 23 |
0.499 (1.00) |
0.137 (1.00) |
0.925 (1.00) |
0.364 (1.00) |
0.625 (1.00) |
0.332 (1.00) |
0.667 (1.00) |
0.384 (1.00) |
P value = 0.000546 (Fisher's exact test), Q value = 0.17
Table S1. Gene #8: '4q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
| nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4 |
|---|---|---|---|---|
| ALL | 10 | 22 | 4 | 19 |
| 4Q MUTATED | 10 | 17 | 0 | 9 |
| 4Q WILD-TYPE | 0 | 5 | 4 | 10 |
Figure S1. Get High-res Image Gene #8: '4q' versus Molecular Subtype #5: 'MIRSEQ_CNMF'
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Copy number data file = transformed.cor.cli.txt
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Molecular subtype file = UCS-TP.transferedmergedcluster.txt
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Number of patients = 56
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Number of significantly focal cnvs = 40
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Number of molecular subtypes = 8
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Exclude genes that fewer than K tumors have alterations, K = 3
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 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 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.