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 |
| ENPP5 | ENSG00000112796 | 0.00 | 0.00 | 0 | 0 |
| LY86 | ENSG00000112799 | 0.00 | 0.00 | 0 | 0 |
| PRSS16 | ENSG00000112812 | 0.00 | 0.00 | 0 | 0 |
| BRD8 | ENSG00000112983 | 0.28 | 0.12 | 1 | 1 |
| HBEGF | ENSG00000113070 | 0.00 | 0.14 | 0 | 1 |
| SLC4A9 | ENSG00000113073 | 0.00 | 0.00 | 0 | 0 |
| LOX | ENSG00000113083 | 0.25 | 0.12 | 1 | 1 |
| GZMK | ENSG00000113088 | 0.00 | 0.00 | 0 | 0 |
| SPARC | ENSG00000113140 | 0.00 | 0.00 | 0 | 0 |
| HMGCR | ENSG00000113161 | 0.00 | 0.87 | 0 | 2 |
| PDE8B | ENSG00000113231 | 0.00 | 0.86 | 0 | 2 |
| CLK4 | ENSG00000113240 | 0.33 | 0.12 | 1 | 1 |
| GRM6 | ENSG00000113262 | 0.00 | 0.00 | 0 | 0 |
| IL12B | ENSG00000113302 | 0.00 | 0.00 | 0 | 0 |
| BTNL8 | ENSG00000113303 | 0.00 | 0.00 | 0 | 0 |
| GABRG2 | ENSG00000113327 | 0.00 | 0.00 | 0 | 0 |
| TARS | ENSG00000113407 | 0.17 | 0.00 | 1 | 0 |
| IL4 | ENSG00000113520 | 0.00 | 0.00 | 0 | 0 |
| IL5 | ENSG00000113525 | 0.00 | 0.00 | 0 | 0 |
| FGF1 | ENSG00000113578 | 0.00 | 0.15 | 0 | 1 |
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