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 |
| CAPZA1 | ENSG00000116489 | 0.00 | 0.62 | 0 | 3 |
| PRG4 | ENSG00000116690 | 0.00 | 0.00 | 0 | 0 |
| SLC35D1 | ENSG00000116704 | 0.00 | 0.00 | 0 | 0 |
| PLA2G4A | ENSG00000116711 | 0.00 | 0.00 | 0 | 0 |
| OLFML3 | ENSG00000116774 | 0.00 | 0.16 | 0 | 1 |
| TNNI3K | ENSG00000116783 | 0.00 | 0.00 | 0 | 0 |
| CFHR3 | ENSG00000116785 | 0.00 | 0.00 | 0 | 0 |
| CD58 | ENSG00000116815 | 0.00 | 0.93 | 0 | 5 |
| BMP8B | ENSG00000116985 | 0.63 | 0.00 | 3 | 0 |
| ZP4 | ENSG00000116996 | 0.00 | 0.00 | 0 | 0 |
| KCNQ4 | ENSG00000117013 | 0.14 | 0.00 | 1 | 0 |
| CD48 | ENSG00000117091 | 0.00 | 0.00 | 0 | 0 |
| MFAP2 | ENSG00000117122 | 0.00 | 0.11 | 0 | 1 |
| CTBS | ENSG00000117151 | 0.00 | 0.00 | 0 | 0 |
| PLA2G2D | ENSG00000117215 | 0.00 | 0.20 | 0 | 1 |
| CD160 | ENSG00000117281 | 0.00 | 0.00 | 0 | 0 |
| GALE | ENSG00000117308 | 0.00 | 0.75 | 0 | 4 |
| MPL | ENSG00000117400 | 0.00 | 0.00 | 0 | 0 |
| ARTN | ENSG00000117407 | 0.00 | 0.00 | 0 | 0 |
| ATP6V0B | ENSG00000117410 | 0.00 | 0.00 | 0 | 0 |
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