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 |
| CD6 | ENSG00000013725 | 0.00 | 0.00 | 0 | 0 |
| YAF2 | ENSG00000015153 | 0.00 | 0.00 | 0 | 0 |
| NPC1L1 | ENSG00000015520 | 0.00 | 0.00 | 0 | 0 |
| CLCA4 | ENSG00000016602 | 0.00 | 0.00 | 0 | 0 |
| SLC11A1 | ENSG00000018280 | 0.00 | 0.00 | 0 | 0 |
| ATP1A2 | ENSG00000018625 | 0.00 | 0.00 | 0 | 0 |
| VSIG2 | ENSG00000019102 | 0.00 | 0.17 | 0 | 1 |
| CYP24A1 | ENSG00000019186 | 0.00 | 0.00 | 0 | 0 |
| CD74 | ENSG00000019582 | 0.30 | 0.14 | 1 | 1 |
| SLC45A4 | ENSG00000022567 | 0.72 | 0.00 | 2 | 0 |
| RNASET2 | ENSG00000026297 | 0.00 | 0.90 | 0 | 4 |
| BTN3A1 | ENSG00000026950 | 0.00 | 0.00 | 0 | 0 |
| IBSP | ENSG00000029559 | 0.00 | 0.00 | 0 | 0 |
| BAK1 | ENSG00000030110 | 0.00 | 0.00 | 0 | 0 |
| MYOC | ENSG00000034971 | 0.00 | 0.00 | 0 | 0 |
| OTC | ENSG00000036473 | 0.00 | 0.00 | 0 | 0 |
| SLC18A1 | ENSG00000036565 | 0.00 | 0.12 | 0 | 1 |
| TUBG2 | ENSG00000037042 | 0.00 | 0.32 | 0 | 2 |
| PI4K2B | ENSG00000038210 | 0.00 | 0.00 | 0 | 0 |
| TLL1 | ENSG00000038295 | 0.00 | 0.00 | 0 | 0 |
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