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 |
| FBXL19 | ENSG00000099364 | 0.26 | 0.00 | 2 | 0 |
| BMPR1A | ENSG00000107779 | 0.00 | 0.00 | 0 | 0 |
| PDE3A | ENSG00000172572 | 0.00 | 0.00 | 0 | 0 |
| A2M | ENSG00000175899 | 0.00 | 0.00 | 0 | 0 |
| BMP2 | ENSG00000125845 | 0.00 | 0.00 | 0 | 0 |
| CETP | ENSG00000087237 | 0.00 | 0.00 | 0 | 0 |
| SLC16A12 | ENSG00000152779 | 0.00 | 0.00 | 0 | 0 |
| MBTPS1 | ENSG00000140943 | 0.00 | 0.79 | 0 | 4 |
| SECTM1 | ENSG00000141574 | 0.00 | 0.00 | 0 | 0 |
| CDK12 | ENSG00000167258 | 0.00 | 0.00 | 0 | 0 |
| COL27A1 | ENSG00000196739 | 0.00 | 0.00 | 0 | 0 |
| TDP1 | ENSG00000042088 | 0.00 | 0.51 | 0 | 2 |
| ACVR1 | ENSG00000115170 | 0.00 | 0.00 | 0 | 0 |
| DAPK2 | ENSG00000035664 | 0.00 | 0.00 | 0 | 0 |
| BCHE | ENSG00000114200 | 0.00 | 0.00 | 0 | 0 |
| KCNN4 | ENSG00000104783 | 0.00 | 0.00 | 0 | 0 |
| EPOR | ENSG00000187266 | 0.00 | 0.00 | 0 | 0 |
| COL18A1 | ENSG00000182871 | 0.10 | 0.18 | 1 | 1 |
| LTF | ENSG00000012223 | 0.00 | 0.34 | 0 | 2 |
| TRPC6 | ENSG00000137672 | 0.00 | 0.00 | 0 | 0 |
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