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 |
| ADCY8 | ENSG00000155897 | 0.20 | 0.00 | 1 | 0 |
| VEGFA | ENSG00000112715 | 1.08 | 0.00 | 3 | 0 |
| MST1R | ENSG00000164078 | 0.00 | 0.35 | 0 | 2 |
| CXADR | ENSG00000154639 | 0.00 | 0.13 | 0 | 1 |
| ATIC | ENSG00000138363 | 0.00 | 0.82 | 0 | 4 |
| ATP2A3 | ENSG00000074370 | 0.00 | 0.12 | 0 | 1 |
| SLC17A9 | ENSG00000101194 | 0.30 | 0.00 | 2 | 0 |
| EPM2A | ENSG00000112425 | 0.00 | 0.59 | 0 | 4 |
| ENC1 | ENSG00000171617 | 0.00 | 0.72 | 0 | 1 |
| SMOC1 | ENSG00000198732 | 0.00 | 0.11 | 0 | 1 |
| SLC36A1 | ENSG00000123643 | 0.31 | 0.14 | 1 | 1 |
| EFNA5 | ENSG00000184349 | 0.00 | 0.00 | 0 | 0 |
| KDM5A | ENSG00000073614 | 1.79 | 0.00 | 6 | 0 |
| CD2 | ENSG00000116824 | 0.00 | 0.00 | 0 | 0 |
| CAPN3 | ENSG00000092529 | 0.00 | 0.00 | 0 | 0 |
| CHST1 | ENSG00000175264 | 0.00 | 0.00 | 0 | 0 |
| ADAMTS14 | ENSG00000138316 | 0.00 | 0.00 | 0 | 0 |
| TRIB1 | ENSG00000173334 | 1.47 | 0.00 | 5 | 0 |
| CYP51A1 | ENSG00000001630 | 0.91 | 0.00 | 3 | 0 |
| APLP2 | ENSG00000084234 | 0.00 | 1.42 | 0 | 7 |
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