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 |
| UQCRC2 | ENSG00000140740 | 0.00 | 0.00 | 0 | 0 |
| ABCB8 | ENSG00000197150 | 0.10 | 0.19 | 1 | 1 |
| SNAP29 | ENSG00000099940 | 0.58 | 0.00 | 2 | 0 |
| ADGRB1 | ENSG00000181790 | 0.74 | 0.00 | 2 | 0 |
| GGT1 | ENSG00000100031 | 0.00 | 0.00 | 0 | 0 |
| SLC35F2 | ENSG00000110660 | 0.00 | 0.11 | 0 | 1 |
| MRC2 | ENSG00000011028 | 0.24 | 0.00 | 1 | 0 |
| PIP5K1A | ENSG00000143398 | 2.46 | 0.00 | 9 | 0 |
| LTBP3 | ENSG00000168056 | 0.18 | 0.00 | 1 | 0 |
| FMO4 | ENSG00000076258 | 0.00 | 0.00 | 0 | 0 |
| SEMA3E | ENSG00000170381 | 0.00 | 0.00 | 0 | 0 |
| NALCN | ENSG00000102452 | 0.13 | 0.00 | 1 | 0 |
| SFMBT2 | ENSG00000198879 | 0.17 | 0.00 | 1 | 0 |
| THBS4 | ENSG00000113296 | 0.00 | 0.00 | 0 | 0 |
| LOXL3 | ENSG00000115318 | 0.00 | 0.00 | 0 | 0 |
| C4BPA | ENSG00000123838 | 0.00 | 0.00 | 0 | 0 |
| GZMA | ENSG00000145649 | 0.00 | 0.00 | 0 | 0 |
| C7 | ENSG00000112936 | 0.00 | 0.00 | 0 | 0 |
| JAK1 | ENSG00000162434 | 0.00 | 0.00 | 0 | 0 |
| MLLT6 | ENSG00000275023 | 0.00 | 0.00 | 0 | 0 |
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