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 |
| HLA-DPA1 | ENSG00000231389 | 0.00 | 0.00 | 0 | 0 |
| CASR | ENSG00000036828 | 0.00 | 0.00 | 0 | 0 |
| SLC38A2 | ENSG00000134294 | 0.43 | 0.00 | 1 | 0 |
| DEAF1 | ENSG00000177030 | 0.00 | 1.06 | 0 | 5 |
| NPSR1 | ENSG00000187258 | 0.00 | 0.00 | 0 | 0 |
| ACVRL1 | ENSG00000139567 | 0.00 | 0.00 | 0 | 0 |
| IL17RA | ENSG00000177663 | 0.00 | 0.13 | 0 | 1 |
| HFE | ENSG00000010704 | 0.00 | 0.00 | 0 | 0 |
| NCOA3 | ENSG00000124151 | 0.12 | 0.00 | 1 | 0 |
| SLC23A2 | ENSG00000089057 | 0.00 | 0.00 | 0 | 0 |
| PRMT2 | ENSG00000160310 | 0.10 | 0.35 | 1 | 2 |
| SUMF1 | ENSG00000144455 | 0.00 | 0.52 | 0 | 3 |
| MAP3K3 | ENSG00000198909 | 0.82 | 0.00 | 4 | 0 |
| BAHD1 | ENSG00000140320 | 0.00 | 0.68 | 0 | 3 |
| PRKD2 | ENSG00000105287 | 0.00 | 0.52 | 0 | 2 |
| FPGS | ENSG00000136877 | 0.00 | 0.11 | 0 | 1 |
| CCS | ENSG00000173992 | 0.28 | 0.00 | 1 | 0 |
| SPSB2 | ENSG00000111671 | 0.00 | 0.00 | 0 | 0 |
| CHST3 | ENSG00000122863 | 0.00 | 0.00 | 0 | 0 |
| DUSP3 | ENSG00000108861 | 0.00 | 0.17 | 0 | 1 |
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