Copy Number
The putative cancer-associated PDGs driven by SCNAs in each cancer type were identified by four criteria: 1) located in a peak region of a significantly recurrent focal SNCA locus estimated by the genomic identification of significant targets in cancer (GISTIC2) algorithm, (q≤0.25); 2) altered with high frequency and large amplitude (G-score ≥0.1); 3) mRNA reliably detected in at least 10% of tumor specimens in the given cancer type (90th percentile of FPKM value ≥1); and 4) mRNA significantly and positively correlated with copy numbers (Pearson P-value less than 0.001).
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| Overall_Gscore | No. of Cancer Types | ||||
| HGNC Symbol | Ensembl Gene ID | Amplification | Deletion | Amplification | Deletion |
| PARP3 | ENSG00000041880 | 0.00 | 0.69 | 0 | 4 |
| SLC44A5 | ENSG00000137968 | 0.00 | 0.00 | 0 | 0 |
| SLK | ENSG00000065613 | 0.00 | 0.61 | 0 | 3 |
| LPAR6 | ENSG00000139679 | 0.00 | 1.63 | 0 | 5 |
| AZIN1 | ENSG00000155096 | 0.57 | 0.00 | 2 | 0 |
| TNKS | ENSG00000173273 | 0.00 | 0.50 | 0 | 3 |
| BAD | ENSG00000002330 | 0.11 | 0.00 | 1 | 0 |
| CASP9 | ENSG00000132906 | 0.00 | 2.14 | 0 | 6 |
| KDM5C | ENSG00000126012 | 0.00 | 0.00 | 0 | 0 |
| KLHL21 | ENSG00000162413 | 0.00 | 1.20 | 0 | 5 |
| CAMKMT | ENSG00000143919 | 0.12 | 0.00 | 1 | 0 |
| C3AR1 | ENSG00000171860 | 0.00 | 0.00 | 0 | 0 |
| PKD2 | ENSG00000118762 | 0.00 | 0.11 | 0 | 1 |
| NQO2 | ENSG00000124588 | 0.41 | 0.37 | 2 | 2 |
| KLK11 | ENSG00000167757 | 0.00 | 0.00 | 0 | 0 |
| GSN | ENSG00000148180 | 0.00 | 0.00 | 0 | 0 |
| DAG1 | ENSG00000173402 | 0.00 | 0.71 | 0 | 4 |
| LSS | ENSG00000160285 | 0.10 | 0.36 | 1 | 2 |
| MAP3K13 | ENSG00000073803 | 0.41 | 0.00 | 2 | 0 |
| HCK | ENSG00000101336 | 0.00 | 0.00 | 0 | 0 |
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