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 |
| PRDM6 | ENSG00000061455 | 0.00 | 0.12 | 0 | 1 |
| SLC5A9 | ENSG00000117834 | 0.00 | 0.00 | 0 | 0 |
| CSTA | ENSG00000121552 | 0.00 | 0.00 | 0 | 0 |
| CPN1 | ENSG00000120054 | 0.00 | 0.00 | 0 | 0 |
| SLC27A6 | ENSG00000113396 | 0.00 | 0.00 | 0 | 0 |
| MORC2 | ENSG00000133422 | 0.23 | 0.00 | 1 | 0 |
| KCNK3 | ENSG00000171303 | 0.00 | 0.00 | 0 | 0 |
| VASN | ENSG00000168140 | 0.00 | 0.00 | 0 | 0 |
| FKBP5 | ENSG00000096060 | 0.00 | 0.00 | 0 | 0 |
| NR1I2 | ENSG00000144852 | 0.00 | 0.00 | 0 | 0 |
| CAPN2 | ENSG00000162909 | 0.00 | 0.23 | 0 | 1 |
| GPC4 | ENSG00000076716 | 0.00 | 0.00 | 0 | 0 |
| EGLN2 | ENSG00000269858 | 0.00 | 0.00 | 0 | 0 |
| CYLD | ENSG00000083799 | 0.00 | 0.00 | 0 | 0 |
| ANXA1 | ENSG00000135046 | 0.00 | 0.00 | 0 | 0 |
| KCNC1 | ENSG00000129159 | 0.00 | 0.00 | 0 | 0 |
| PTPRS | ENSG00000105426 | 0.00 | 0.00 | 0 | 0 |
| PSKH1 | ENSG00000159792 | 0.33 | 0.47 | 2 | 2 |
| TRIM24 | ENSG00000122779 | 0.33 | 0.00 | 2 | 0 |
| PDGFD | ENSG00000170962 | 0.00 | 0.00 | 0 | 0 |
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