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 |
| NUAK1 | ENSG00000074590 | 0.00 | 0.00 | 0 | 0 |
| TNFSF13B | ENSG00000102524 | 0.00 | 0.00 | 0 | 0 |
| PNCK | ENSG00000130822 | 0.00 | 0.00 | 0 | 0 |
| HHIPL1 | ENSG00000182218 | 0.00 | 0.00 | 0 | 0 |
| RHCG | ENSG00000140519 | 0.00 | 0.00 | 0 | 0 |
| PDE7A | ENSG00000205268 | 0.55 | 0.00 | 3 | 0 |
| RXFP1 | ENSG00000171509 | 0.00 | 0.00 | 0 | 0 |
| GBA | ENSG00000177628 | 0.76 | 0.00 | 4 | 0 |
| SLC18B1 | ENSG00000146409 | 0.00 | 0.00 | 0 | 0 |
| SEMA3D | ENSG00000153993 | 0.00 | 0.00 | 0 | 0 |
| PTPN4 | ENSG00000088179 | 0.31 | 0.00 | 1 | 0 |
| SP140 | ENSG00000079263 | 0.00 | 0.69 | 0 | 3 |
| COL12A1 | ENSG00000111799 | 0.00 | 0.00 | 0 | 0 |
| PAK2 | ENSG00000180370 | 0.18 | 0.12 | 1 | 1 |
| FMO1 | ENSG00000010932 | 0.00 | 0.00 | 0 | 0 |
| RIPK2 | ENSG00000104312 | 0.50 | 0.00 | 2 | 0 |
| TIE1 | ENSG00000066056 | 0.00 | 0.00 | 0 | 0 |
| BRWD1 | ENSG00000185658 | 0.15 | 0.00 | 1 | 0 |
| CRISP3 | ENSG00000096006 | 0.00 | 0.00 | 0 | 0 |
| SLC1A3 | ENSG00000079215 | 0.00 | 0.00 | 0 | 0 |
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