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 |
| BMP10 | ENSG00000163217 | 0.00 | 0.00 | 0 | 0 |
| PGLYRP4 | ENSG00000163218 | 0.00 | 0.00 | 0 | 0 |
| S100A9 | ENSG00000163220 | 0.00 | 0.00 | 0 | 0 |
| S100A12 | ENSG00000163221 | 0.00 | 0.00 | 0 | 0 |
| TGFA | ENSG00000163235 | 0.00 | 0.00 | 0 | 0 |
| FZD5 | ENSG00000163251 | 0.00 | 0.00 | 0 | 0 |
| NPPC | ENSG00000163273 | 0.00 | 0.00 | 0 | 0 |
| ALPP | ENSG00000163283 | 0.00 | 0.00 | 0 | 0 |
| GABRG1 | ENSG00000163285 | 0.00 | 0.00 | 0 | 0 |
| ALPPL2 | ENSG00000163286 | 0.00 | 0.00 | 0 | 0 |
| ALPI | ENSG00000163295 | 0.00 | 0.00 | 0 | 0 |
| ANTXR2 | ENSG00000163297 | 0.00 | 0.00 | 0 | 0 |
| COL6A3 | ENSG00000163359 | 0.00 | 0.42 | 0 | 2 |
| KBTBD8 | ENSG00000163376 | 0.00 | 0.00 | 0 | 0 |
| FAM19A4 | ENSG00000163377 | 0.00 | 0.00 | 0 | 0 |
| APOA1BP | ENSG00000163382 | 0.64 | 0.00 | 4 | 0 |
| POGLUT1 | ENSG00000163389 | 0.00 | 0.00 | 0 | 0 |
| CCKAR | ENSG00000163394 | 0.00 | 0.00 | 0 | 0 |
| SLC15A2 | ENSG00000163406 | 0.00 | 0.00 | 0 | 0 |
| PROK2 | ENSG00000163421 | 0.00 | 0.00 | 0 | 0 |
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