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 |
| ING4 | ENSG00000111653 | 0.60 | 0.00 | 1 | 0 |
| SIRT2 | ENSG00000068903 | 0.76 | 0.00 | 1 | 0 |
| MAP3K4 | ENSG00000085511 | 0.00 | 0.97 | 0 | 4 |
| GRIA1 | ENSG00000155511 | 0.00 | 0.00 | 0 | 0 |
| HSD17B13 | ENSG00000170509 | 0.00 | 0.00 | 0 | 0 |
| DMPK | ENSG00000104936 | 0.00 | 0.30 | 0 | 1 |
| ADAM22 | ENSG00000008277 | 0.00 | 0.00 | 0 | 0 |
| SERPINB6 | ENSG00000124570 | 0.62 | 0.14 | 3 | 1 |
| NRXN1 | ENSG00000179915 | 0.00 | 0.00 | 0 | 0 |
| CD151 | ENSG00000177697 | 0.00 | 0.57 | 0 | 4 |
| APOE | ENSG00000130203 | 0.00 | 0.30 | 0 | 1 |
| PAH | ENSG00000171759 | 0.00 | 0.00 | 0 | 0 |
| BACE1 | ENSG00000186318 | 0.00 | 0.86 | 0 | 4 |
| ADAM17 | ENSG00000151694 | 0.17 | 0.16 | 1 | 1 |
| WIF1 | ENSG00000156076 | 0.00 | 0.00 | 0 | 0 |
| ACE | ENSG00000159640 | 0.00 | 0.00 | 0 | 0 |
| KEL | ENSG00000197993 | 0.00 | 0.00 | 0 | 0 |
| SLC1A6 | ENSG00000105143 | 0.00 | 0.00 | 0 | 0 |
| AK2 | ENSG00000004455 | 0.00 | 0.00 | 0 | 0 |
| COL21A1 | ENSG00000124749 | 0.00 | 0.00 | 0 | 0 |
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