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 |
| CA5A | ENSG00000174990 | 0.00 | 0.00 | 0 | 0 |
| DYRK2 | ENSG00000127334 | 0.25 | 0.00 | 1 | 0 |
| PHF19 | ENSG00000119403 | 0.00 | 0.00 | 0 | 0 |
| B4GALT1 | ENSG00000086062 | 0.00 | 0.00 | 0 | 0 |
| RHBDD1 | ENSG00000144468 | 0.00 | 1.19 | 0 | 5 |
| SETD5 | ENSG00000168137 | 0.00 | 0.18 | 0 | 1 |
| STK32B | ENSG00000152953 | 0.00 | 0.00 | 0 | 0 |
| DPP9 | ENSG00000142002 | 0.00 | 0.00 | 0 | 0 |
| XIAP | ENSG00000101966 | 0.00 | 0.00 | 0 | 0 |
| LY96 | ENSG00000154589 | 0.22 | 0.00 | 1 | 0 |
| GUCY1A3 | ENSG00000164116 | 0.00 | 0.00 | 0 | 0 |
| PDIA5 | ENSG00000065485 | 0.00 | 0.00 | 0 | 0 |
| ATP10D | ENSG00000145246 | 0.00 | 0.00 | 0 | 0 |
| TRPM1 | ENSG00000134160 | 0.00 | 0.00 | 0 | 0 |
| ESRRA | ENSG00000173153 | 0.11 | 0.00 | 1 | 0 |
| MAP3K6 | ENSG00000142733 | 0.00 | 0.44 | 0 | 2 |
| YME1L1 | ENSG00000136758 | 0.00 | 0.00 | 0 | 0 |
| PDE8A | ENSG00000073417 | 0.34 | 0.00 | 2 | 0 |
| OTUD5 | ENSG00000068308 | 0.49 | 0.00 | 1 | 0 |
| ALDH16A1 | ENSG00000161618 | 0.26 | 0.49 | 1 | 2 |
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