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 |
| MAP3K7 | ENSG00000135341 | 0.00 | 0.44 | 0 | 3 |
| NPR3 | ENSG00000113389 | 0.00 | 0.00 | 0 | 0 |
| SMPD3 | ENSG00000103056 | 0.31 | 0.00 | 2 | 0 |
| ABCA6 | ENSG00000154262 | 0.00 | 0.00 | 0 | 0 |
| NFKB1 | ENSG00000109320 | 0.00 | 0.13 | 0 | 1 |
| PTGER3 | ENSG00000050628 | 0.00 | 0.00 | 0 | 0 |
| MUC1 | ENSG00000185499 | 0.00 | 0.00 | 0 | 0 |
| LYN | ENSG00000254087 | 0.20 | 0.00 | 1 | 0 |
| ATM | ENSG00000149311 | 0.00 | 0.44 | 0 | 3 |
| IL1R2 | ENSG00000115590 | 0.00 | 0.00 | 0 | 0 |
| APOB | ENSG00000084674 | 0.18 | 0.00 | 1 | 0 |
| ST3GAL4 | ENSG00000110080 | 0.12 | 0.86 | 1 | 4 |
| DPYD | ENSG00000188641 | 0.00 | 0.52 | 0 | 2 |
| PTPN3 | ENSG00000070159 | 0.00 | 0.00 | 0 | 0 |
| SLC2A1 | ENSG00000117394 | 0.00 | 0.00 | 0 | 0 |
| PLOD1 | ENSG00000083444 | 0.00 | 0.54 | 0 | 3 |
| GAK | ENSG00000178950 | 0.74 | 0.00 | 3 | 0 |
| RELN | ENSG00000189056 | 0.00 | 0.00 | 0 | 0 |
| AKR1C1 | ENSG00000187134 | 0.32 | 0.00 | 2 | 0 |
| AMPD2 | ENSG00000116337 | 0.00 | 0.47 | 0 | 2 |
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