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 |
| MLX | ENSG00000108788 | 0.00 | 0.20 | 0 | 1 |
| CNTNAP1 | ENSG00000108797 | 0.00 | 0.00 | 0 | 0 |
| VAT1 | ENSG00000108828 | 0.00 | 0.00 | 0 | 0 |
| PPY | ENSG00000108849 | 0.00 | 0.00 | 0 | 0 |
| EFNB3 | ENSG00000108947 | 0.00 | 0.00 | 0 | 0 |
| FAM20A | ENSG00000108950 | 0.00 | 0.00 | 0 | 0 |
| DHRS7B | ENSG00000109016 | 0.17 | 0.19 | 1 | 1 |
| GABRA4 | ENSG00000109158 | 0.00 | 0.00 | 0 | 0 |
| GNRHR | ENSG00000109163 | 0.00 | 0.00 | 0 | 0 |
| UGT2B10 | ENSG00000109181 | 0.00 | 0.00 | 0 | 0 |
| SULT1E1 | ENSG00000109193 | 0.00 | 0.00 | 0 | 0 |
| ODAM | ENSG00000109205 | 0.00 | 0.00 | 0 | 0 |
| SMR3A | ENSG00000109208 | 0.00 | 0.00 | 0 | 0 |
| NMU | ENSG00000109255 | 0.62 | 0.00 | 2 | 0 |
| PF4V1 | ENSG00000109272 | 0.00 | 0.00 | 0 | 0 |
| AREG | ENSG00000109321 | 0.00 | 0.00 | 0 | 0 |
| UCP1 | ENSG00000109424 | 0.00 | 0.00 | 0 | 0 |
| IL2 | ENSG00000109471 | 0.00 | 0.00 | 0 | 0 |
| SOD3 | ENSG00000109610 | 0.00 | 0.00 | 0 | 0 |
| CPZ | ENSG00000109625 | 0.00 | 0.00 | 0 | 0 |
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