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 |
| CASP3 | ENSG00000164305 | 0.00 | 1.25 | 0 | 8 |
| ERAP1 | ENSG00000164307 | 0.00 | 0.12 | 0 | 1 |
| EGFLAM | ENSG00000164318 | 0.00 | 0.00 | 0 | 0 |
| CARTPT | ENSG00000164326 | 0.00 | 0.00 | 0 | 0 |
| TLR3 | ENSG00000164342 | 0.00 | 1.04 | 0 | 6 |
| KLKB1 | ENSG00000164344 | 0.00 | 0.00 | 0 | 0 |
| IL3 | ENSG00000164399 | 0.00 | 0.00 | 0 | 0 |
| CSF2 | ENSG00000164400 | 0.00 | 0.00 | 0 | 0 |
| GDF9 | ENSG00000164404 | 0.00 | 0.00 | 0 | 0 |
| LEAP2 | ENSG00000164406 | 0.28 | 0.00 | 1 | 0 |
| FABP7 | ENSG00000164434 | 0.00 | 0.00 | 0 | 0 |
| IL22RA2 | ENSG00000164485 | 0.00 | 0.00 | 0 | 0 |
| IL31RA | ENSG00000164509 | 0.00 | 0.00 | 0 | 0 |
| PI16 | ENSG00000164530 | 0.00 | 0.00 | 0 | 0 |
| DAGLB | ENSG00000164535 | 0.58 | 0.39 | 4 | 1 |
| STK17A | ENSG00000164543 | 0.00 | 0.00 | 0 | 0 |
| HCN1 | ENSG00000164588 | 0.00 | 0.00 | 0 | 0 |
| GPR85 | ENSG00000164604 | 0.00 | 0.00 | 0 | 0 |
| SLC29A4 | ENSG00000164638 | 0.32 | 0.41 | 2 | 1 |
| STEAP1 | ENSG00000164647 | 0.13 | 0.00 | 1 | 0 |
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