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 |
| PSG2 | ENSG00000242221 | 0.00 | 0.00 | 0 | 0 |
| BGLAP | ENSG00000242252 | 0.48 | 0.00 | 3 | 0 |
| UGT1A8 | ENSG00000242366 | 0.00 | 0.00 | 0 | 0 |
| IGKV1-39 | ENSG00000242371 | 0.00 | 0.00 | 0 | 0 |
| SERPINB10 | ENSG00000242550 | 0.00 | 0.00 | 0 | 0 |
| DECR2 | ENSG00000242612 | 0.00 | 0.00 | 0 | 0 |
| CNTF | ENSG00000242689 | 0.00 | 0.00 | 0 | 0 |
| ABCC13 | ENSG00000243064 | 0.00 | 0.00 | 0 | 0 |
| IGKV2-30 | ENSG00000243238 | 0.00 | 0.00 | 0 | 0 |
| IGKV2D-29 | ENSG00000243264 | 0.00 | 0.00 | 0 | 0 |
| IGKV1-5 | ENSG00000243466 | 0.00 | 0.00 | 0 | 0 |
| AMY2A | ENSG00000243480 | 0.00 | 0.00 | 0 | 0 |
| TNFRSF6B | ENSG00000243509 | 0.00 | 0.00 | 0 | 0 |
| PLA2G4B | ENSG00000243708 | 0.00 | 0.11 | 0 | 1 |
| LEFTY1 | ENSG00000243709 | 0.00 | 0.00 | 0 | 0 |
| KIR2DL3 | ENSG00000243772 | 0.00 | 0.00 | 0 | 0 |
| OR2A7 | ENSG00000243896 | 0.00 | 0.00 | 0 | 0 |
| ACY1 | ENSG00000243989 | 0.00 | 0.52 | 0 | 3 |
| DDOST | ENSG00000244038 | 0.00 | 1.10 | 0 | 6 |
| GSTA2 | ENSG00000244067 | 0.00 | 0.00 | 0 | 0 |
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