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 |
| AMY2B | ENSG00000240038 | 0.00 | 0.23 | 0 | 2 |
| PSMB9 | ENSG00000240065 | 0.00 | 0.00 | 0 | 0 |
| UGT1A5 | ENSG00000240224 | 0.00 | 0.00 | 0 | 0 |
| PPIL3 | ENSG00000240344 | 0.14 | 0.00 | 1 | 0 |
| KIR3DL2 | ENSG00000240403 | 0.00 | 0.00 | 0 | 0 |
| C1QTNF9 | ENSG00000240654 | 0.00 | 0.00 | 0 | 0 |
| MIF | ENSG00000240972 | 0.00 | 0.00 | 0 | 0 |
| HLA-DOB | ENSG00000241106 | 0.00 | 0.00 | 0 | 0 |
| UGT1A9 | ENSG00000241119 | 0.00 | 0.00 | 0 | 0 |
| OR14A2 | ENSG00000241128 | 0.00 | 0.00 | 0 | 0 |
| TDGF1 | ENSG00000241186 | 0.00 | 0.00 | 0 | 0 |
| IGKV1D-16 | ENSG00000241244 | 0.00 | 0.00 | 0 | 0 |
| IGKV3-11 | ENSG00000241351 | 0.00 | 0.00 | 0 | 0 |
| CD302 | ENSG00000241399 | 0.00 | 0.00 | 0 | 0 |
| EGFL8 | ENSG00000241404 | 0.00 | 0.00 | 0 | 0 |
| ATP5J2 | ENSG00000241468 | 0.15 | 0.00 | 1 | 0 |
| CORT | ENSG00000241563 | 0.00 | 0.00 | 0 | 0 |
| UGT1A1 | ENSG00000241635 | 0.00 | 0.00 | 0 | 0 |
| KIR3DL3 | ENSG00000242019 | 0.00 | 0.00 | 0 | 0 |
| OR51B5 | ENSG00000242180 | 0.00 | 0.00 | 0 | 0 |
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