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 |
| HIPK3 | ENSG00000110422 | 0.41 | 0.00 | 2 | 0 |
| TEK | ENSG00000120156 | 0.00 | 0.00 | 0 | 0 |
| PHKG1 | ENSG00000164776 | 0.00 | 0.00 | 0 | 0 |
| CYP2C18 | ENSG00000108242 | 0.00 | 0.00 | 0 | 0 |
| NEK3 | ENSG00000136098 | 0.00 | 0.50 | 0 | 3 |
| EPHB1 | ENSG00000154928 | 0.00 | 0.00 | 0 | 0 |
| ADCK1 | ENSG00000063761 | 0.00 | 0.42 | 0 | 2 |
| CEP41 | ENSG00000106477 | 0.13 | 0.14 | 1 | 1 |
| MERTK | ENSG00000153208 | 0.00 | 0.00 | 0 | 0 |
| LAMC3 | ENSG00000050555 | 0.00 | 0.00 | 0 | 0 |
| TLK2 | ENSG00000146872 | 0.72 | 0.00 | 3 | 0 |
| ANXA2 | ENSG00000182718 | 0.00 | 0.00 | 0 | 0 |
| SLC13A2 | ENSG00000007216 | 0.00 | 0.00 | 0 | 0 |
| SCN3A | ENSG00000153253 | 0.00 | 0.00 | 0 | 0 |
| IDO1 | ENSG00000131203 | 0.00 | 0.00 | 0 | 0 |
| ADCK5 | ENSG00000173137 | 1.14 | 0.00 | 4 | 0 |
| NGFR | ENSG00000064300 | 0.00 | 0.00 | 0 | 0 |
| SLC16A2 | ENSG00000147100 | 0.00 | 0.00 | 0 | 0 |
| FGG | ENSG00000171557 | 0.00 | 0.00 | 0 | 0 |
| CBX3 | ENSG00000122565 | 0.00 | 0.00 | 0 | 0 |
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