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 |
| ABL2 | ENSG00000143322 | 0.00 | 0.00 | 0 | 0 |
| MTF2 | ENSG00000143033 | 0.00 | 0.63 | 0 | 3 |
| ABCC5 | ENSG00000114770 | 0.39 | 0.00 | 2 | 0 |
| PEBP4 | ENSG00000134020 | 0.00 | 0.24 | 0 | 1 |
| ADAMTS9 | ENSG00000163638 | 0.00 | 0.00 | 0 | 0 |
| NOS2 | ENSG00000007171 | 0.00 | 0.00 | 0 | 0 |
| STRADA | ENSG00000266173 | 0.82 | 0.00 | 4 | 0 |
| RPS6KB1 | ENSG00000108443 | 0.64 | 0.00 | 3 | 0 |
| SLC38A5 | ENSG00000017483 | 0.00 | 0.00 | 0 | 0 |
| NAALADL1 | ENSG00000168060 | 0.00 | 0.00 | 0 | 0 |
| SEMA3C | ENSG00000075223 | 0.00 | 0.00 | 0 | 0 |
| F5 | ENSG00000198734 | 0.00 | 0.00 | 0 | 0 |
| SLC6A9 | ENSG00000196517 | 0.00 | 0.00 | 0 | 0 |
| KDM6A | ENSG00000147050 | 0.00 | 0.35 | 0 | 2 |
| KALRN | ENSG00000160145 | 0.00 | 0.00 | 0 | 0 |
| PLXNB1 | ENSG00000164050 | 0.00 | 0.67 | 0 | 4 |
| ALDH1A1 | ENSG00000165092 | 0.00 | 0.00 | 0 | 0 |
| ABCA7 | ENSG00000064687 | 0.00 | 0.15 | 0 | 1 |
| GDF6 | ENSG00000156466 | 0.00 | 0.00 | 0 | 0 |
| PDE10A | ENSG00000112541 | 0.00 | 0.15 | 0 | 1 |
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