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 |
| TXNDC15 | ENSG00000113621 | 0.28 | 0.00 | 1 | 0 |
| RARS | ENSG00000113643 | 0.32 | 0.21 | 1 | 2 |
| ATP6V0E1 | ENSG00000113732 | 0.33 | 0.10 | 1 | 1 |
| HRG | ENSG00000113905 | 0.00 | 0.00 | 0 | 0 |
| RBP2 | ENSG00000114113 | 0.00 | 0.00 | 0 | 0 |
| RBP1 | ENSG00000114115 | 0.00 | 0.00 | 0 | 0 |
| GRK7 | ENSG00000114124 | 0.00 | 0.00 | 0 | 0 |
| KAT2B | ENSG00000114166 | 0.00 | 0.17 | 0 | 1 |
| SERPINI2 | ENSG00000114204 | 0.00 | 0.00 | 0 | 0 |
| WNT5A | ENSG00000114251 | 0.00 | 0.17 | 0 | 1 |
| HYAL1 | ENSG00000114378 | 0.00 | 0.36 | 0 | 2 |
| CSPG5 | ENSG00000114646 | 0.00 | 0.36 | 0 | 2 |
| ACVR2B | ENSG00000114739 | 0.00 | 0.00 | 0 | 0 |
| AADAC | ENSG00000114771 | 0.00 | 0.00 | 0 | 0 |
| VIPR1 | ENSG00000114812 | 0.00 | 0.00 | 0 | 0 |
| NKTR | ENSG00000114857 | 0.00 | 0.00 | 0 | 0 |
| SPCS1 | ENSG00000114902 | 0.00 | 0.90 | 0 | 5 |
| SLC4A3 | ENSG00000114923 | 0.00 | 0.38 | 0 | 2 |
| TTL | ENSG00000114999 | 0.00 | 0.00 | 0 | 0 |
| IL1A | ENSG00000115008 | 0.00 | 0.00 | 0 | 0 |
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