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 |
| MPZ | ENSG00000158887 | 0.10 | 0.00 | 1 | 0 |
| IFNAR2 | ENSG00000159110 | 0.00 | 0.00 | 0 | 0 |
| SV2A | ENSG00000159164 | 0.40 | 0.00 | 2 | 0 |
| LAD1 | ENSG00000159166 | 0.00 | 0.00 | 0 | 0 |
| STC1 | ENSG00000159167 | 0.00 | 0.00 | 0 | 0 |
| GIP | ENSG00000159224 | 0.00 | 0.00 | 0 | 0 |
| CBR1 | ENSG00000159228 | 0.00 | 0.00 | 0 | 0 |
| ATP13A2 | ENSG00000159363 | 0.00 | 0.79 | 0 | 4 |
| PSMB4 | ENSG00000159377 | 2.40 | 0.00 | 9 | 0 |
| CES5A | ENSG00000159398 | 0.00 | 0.00 | 0 | 0 |
| C1R | ENSG00000159403 | 0.00 | 0.00 | 0 | 0 |
| ALDH4A1 | ENSG00000159423 | 0.00 | 0.68 | 0 | 4 |
| PGLYRP3 | ENSG00000159527 | 0.00 | 0.00 | 0 | 0 |
| ATP6V0D1 | ENSG00000159720 | 0.30 | 0.18 | 2 | 1 |
| AGRP | ENSG00000159723 | 0.00 | 0.00 | 0 | 0 |
| LYPD5 | ENSG00000159871 | 0.00 | 0.29 | 0 | 1 |
| TNFRSF13C | ENSG00000159958 | 0.00 | 0.00 | 0 | 0 |
| OR3A3 | ENSG00000159961 | 0.00 | 0.00 | 0 | 0 |
| PTGIR | ENSG00000160013 | 0.00 | 0.00 | 0 | 0 |
| CALM3 | ENSG00000160014 | 0.14 | 0.51 | 1 | 2 |
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