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 |
| OPN4 | ENSG00000122375 | 0.00 | 0.00 | 0 | 0 |
| PTGFR | ENSG00000122420 | 0.00 | 0.00 | 0 | 0 |
| NPY | ENSG00000122585 | 0.00 | 0.00 | 0 | 0 |
| INHBA | ENSG00000122641 | 0.00 | 0.00 | 0 | 0 |
| FKBP9 | ENSG00000122642 | 0.00 | 0.00 | 0 | 0 |
| RAMP3 | ENSG00000122679 | 0.00 | 0.00 | 0 | 0 |
| SLC25A51 | ENSG00000122696 | 0.00 | 0.11 | 0 | 1 |
| SPINK4 | ENSG00000122711 | 0.00 | 0.00 | 0 | 0 |
| TAF1L | ENSG00000122728 | 0.00 | 0.00 | 0 | 0 |
| PHF24 | ENSG00000122733 | 0.00 | 0.00 | 0 | 0 |
| SFTPA1 | ENSG00000122852 | 0.00 | 0.00 | 0 | 0 |
| PLAU | ENSG00000122861 | 0.00 | 0.00 | 0 | 0 |
| SRGN | ENSG00000122862 | 0.00 | 0.00 | 0 | 0 |
| CISD1 | ENSG00000122873 | 0.00 | 0.00 | 0 | 0 |
| HVCN1 | ENSG00000122986 | 0.00 | 0.00 | 0 | 0 |
| PRDX4 | ENSG00000123131 | 0.29 | 0.00 | 2 | 0 |
| ATP7B | ENSG00000123191 | 0.00 | 0.36 | 0 | 2 |
| GUCY1B2 | ENSG00000123201 | 0.00 | 0.21 | 0 | 1 |
| ITIH5 | ENSG00000123243 | 0.00 | 0.00 | 0 | 0 |
| NR4A1 | ENSG00000123358 | 0.00 | 0.00 | 0 | 0 |
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