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 |
| SLCO1C1 | ENSG00000139155 | 0.00 | 0.00 | 0 | 0 |
| TNFRSF21 | ENSG00000146072 | 0.00 | 0.00 | 0 | 0 |
| AXL | ENSG00000167601 | 0.00 | 0.00 | 0 | 0 |
| KCNN1 | ENSG00000105642 | 0.00 | 0.00 | 0 | 0 |
| RSF1 | ENSG00000048649 | 1.05 | 0.00 | 3 | 0 |
| ALDH7A1 | ENSG00000164904 | 0.25 | 0.00 | 1 | 0 |
| CHD3 | ENSG00000170004 | 0.00 | 0.16 | 0 | 1 |
| KMT2D | ENSG00000167548 | 0.00 | 0.00 | 0 | 0 |
| ALDH1L1 | ENSG00000144908 | 0.00 | 0.00 | 0 | 0 |
| CD5 | ENSG00000110448 | 0.00 | 0.00 | 0 | 0 |
| ADCY5 | ENSG00000173175 | 0.00 | 0.00 | 0 | 0 |
| JMJD1C | ENSG00000171988 | 0.00 | 0.00 | 0 | 0 |
| OLFM4 | ENSG00000102837 | 0.00 | 0.20 | 0 | 1 |
| UGCG | ENSG00000148154 | 0.00 | 0.15 | 0 | 1 |
| NR2F2 | ENSG00000185551 | 0.36 | 0.00 | 2 | 0 |
| C8B | ENSG00000021852 | 0.00 | 0.00 | 0 | 0 |
| SLC39A3 | ENSG00000141873 | 0.00 | 0.88 | 0 | 2 |
| EIF2AK3 | ENSG00000172071 | 0.17 | 0.00 | 1 | 0 |
| KIRREL2 | ENSG00000126259 | 0.00 | 0.00 | 0 | 0 |
| PLCB4 | ENSG00000101333 | 0.00 | 0.00 | 0 | 0 |
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