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 |
| SLC2A8 | ENSG00000136856 | 0.00 | 0.19 | 0 | 1 |
| CSNK1G3 | ENSG00000151292 | 0.25 | 0.13 | 1 | 1 |
| NEK4 | ENSG00000114904 | 0.00 | 0.71 | 0 | 4 |
| BRPF3 | ENSG00000096070 | 0.00 | 0.00 | 0 | 0 |
| ADAM18 | ENSG00000168619 | 0.00 | 0.00 | 0 | 0 |
| MAPK14 | ENSG00000112062 | 0.00 | 0.00 | 0 | 0 |
| NUCB1 | ENSG00000104805 | 0.00 | 0.52 | 0 | 2 |
| IMPA1 | ENSG00000133731 | 0.55 | 0.00 | 3 | 0 |
| HSD17B11 | ENSG00000198189 | 0.00 | 0.11 | 0 | 1 |
| CASK | ENSG00000147044 | 0.12 | 0.00 | 1 | 0 |
| KAT7 | ENSG00000136504 | 0.00 | 0.00 | 0 | 0 |
| CAMK2D | ENSG00000145349 | 0.00 | 0.00 | 0 | 0 |
| FKBP3 | ENSG00000100442 | 0.00 | 0.00 | 0 | 0 |
| SMPD1 | ENSG00000166311 | 0.00 | 0.00 | 0 | 0 |
| SPG7 | ENSG00000197912 | 0.00 | 0.92 | 0 | 6 |
| GFOD2 | ENSG00000141098 | 0.31 | 0.47 | 2 | 2 |
| MANBA | ENSG00000109323 | 0.00 | 0.13 | 0 | 1 |
| FKBP15 | ENSG00000119321 | 0.00 | 0.15 | 0 | 1 |
| ALCAM | ENSG00000170017 | 0.00 | 0.00 | 0 | 0 |
| BRD3 | ENSG00000169925 | 0.00 | 0.25 | 0 | 1 |
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