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 |
| LAG3 | ENSG00000089692 | 0.00 | 0.00 | 0 | 0 |
| LTBP4 | ENSG00000090006 | 0.00 | 0.00 | 0 | 0 |
| LYZ | ENSG00000090382 | 0.00 | 0.00 | 0 | 0 |
| SI | ENSG00000090402 | 0.00 | 0.00 | 0 | 0 |
| DNAJB11 | ENSG00000090520 | 0.43 | 0.00 | 2 | 0 |
| THPO | ENSG00000090534 | 0.22 | 0.00 | 1 | 0 |
| CD209 | ENSG00000090659 | 0.00 | 0.00 | 0 | 0 |
| EFNB1 | ENSG00000090776 | 0.00 | 0.00 | 0 | 0 |
| SLC26A4 | ENSG00000091137 | 0.00 | 0.00 | 0 | 0 |
| SLC26A3 | ENSG00000091138 | 0.00 | 0.00 | 0 | 0 |
| TXNL1 | ENSG00000091164 | 0.12 | 0.10 | 1 | 1 |
| IL5RA | ENSG00000091181 | 0.00 | 0.00 | 0 | 0 |
| pk | ENSG00000091436 | 0.11 | 0.00 | 1 | 0 |
| SLC17A6 | ENSG00000091664 | 0.00 | 0.00 | 0 | 0 |
| ANGPT2 | ENSG00000091879 | 0.00 | 0.00 | 0 | 0 |
| CD200 | ENSG00000091972 | 0.00 | 0.00 | 0 | 0 |
| CMA1 | ENSG00000092009 | 0.00 | 0.00 | 0 | 0 |
| MYH7 | ENSG00000092054 | 0.00 | 0.00 | 0 | 0 |
| OSGEP | ENSG00000092094 | 0.00 | 0.10 | 0 | 1 |
| TGM1 | ENSG00000092295 | 0.00 | 0.00 | 0 | 0 |
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