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 |
| TUFT1 | ENSG00000143367 | 1.92 | 0.00 | 7 | 0 |
| ALDH1A3 | ENSG00000184254 | 0.11 | 0.00 | 1 | 0 |
| CEACAM5 | ENSG00000105388 | 0.00 | 0.00 | 0 | 0 |
| ARID4A | ENSG00000032219 | 0.00 | 0.00 | 0 | 0 |
| HSD11B2 | ENSG00000176387 | 0.00 | 0.00 | 0 | 0 |
| NAPSA | ENSG00000131400 | 0.00 | 0.31 | 0 | 1 |
| MAP4K1 | ENSG00000104814 | 0.54 | 0.00 | 1 | 0 |
| PTPN14 | ENSG00000152104 | 0.00 | 0.39 | 0 | 2 |
| BCAT1 | ENSG00000060982 | 1.23 | 0.00 | 3 | 0 |
| ABCC3 | ENSG00000108846 | 0.00 | 0.00 | 0 | 0 |
| ADCYAP1R1 | ENSG00000078549 | 0.00 | 0.00 | 0 | 0 |
| MMP16 | ENSG00000156103 | 0.00 | 0.00 | 0 | 0 |
| GPC6 | ENSG00000183098 | 0.24 | 0.00 | 1 | 0 |
| LIPG | ENSG00000101670 | 0.00 | 0.00 | 0 | 0 |
| PASK | ENSG00000115687 | 0.00 | 1.45 | 0 | 7 |
| FLRT1 | ENSG00000126500 | 0.00 | 0.00 | 0 | 0 |
| BAMBI | ENSG00000095739 | 0.00 | 0.00 | 0 | 0 |
| LAMA3 | ENSG00000053747 | 0.15 | 0.00 | 1 | 0 |
| MATN3 | ENSG00000132031 | 0.18 | 0.15 | 1 | 1 |
| SCARB1 | ENSG00000073060 | 0.00 | 0.10 | 0 | 1 |
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