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 |
| LALBA | ENSG00000167531 | 0.00 | 0.00 | 0 | 0 |
| CACNB3 | ENSG00000167535 | 0.00 | 0.00 | 0 | 0 |
| TUBA1A | ENSG00000167552 | 0.00 | 0.00 | 0 | 0 |
| LAIR1 | ENSG00000167613 | 0.00 | 0.17 | 0 | 1 |
| LAIR2 | ENSG00000167618 | 0.00 | 0.00 | 0 | 0 |
| KIR3DL1 | ENSG00000167633 | 0.00 | 0.00 | 0 | 0 |
| SPINT2 | ENSG00000167642 | 0.86 | 0.00 | 2 | 0 |
| PSCA | ENSG00000167653 | 0.24 | 0.00 | 1 | 0 |
| LY6D | ENSG00000167656 | 0.00 | 0.00 | 0 | 0 |
| DAPK3 | ENSG00000167657 | 0.00 | 1.16 | 0 | 3 |
| HDGFRP2 | ENSG00000167674 | 0.00 | 0.00 | 0 | 0 |
| SEMA6B | ENSG00000167680 | 0.00 | 0.00 | 0 | 0 |
| SLC43A2 | ENSG00000167703 | 0.00 | 0.00 | 0 | 0 |
| CYB5D2 | ENSG00000167740 | 0.00 | 0.12 | 0 | 1 |
| KLK5 | ENSG00000167754 | 0.00 | 0.00 | 0 | 0 |
| KLK6 | ENSG00000167755 | 0.00 | 0.00 | 0 | 0 |
| KLK13 | ENSG00000167759 | 0.00 | 0.00 | 0 | 0 |
| ANGPTL4 | ENSG00000167772 | 0.00 | 0.00 | 0 | 0 |
| CD320 | ENSG00000167775 | 0.00 | 0.00 | 0 | 0 |
| OR8J3 | ENSG00000167822 | 0.00 | 0.00 | 0 | 0 |
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