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 |
| HUNK | ENSG00000142149 | 0.00 | 0.00 | 0 | 0 |
| KCNC2 | ENSG00000166006 | 0.00 | 0.00 | 0 | 0 |
| MAPK6 | ENSG00000069956 | 0.00 | 0.10 | 0 | 1 |
| VARS2 | ENSG00000137411 | 0.00 | 0.00 | 0 | 0 |
| PHOSPHO1 | ENSG00000173868 | 0.00 | 0.00 | 0 | 0 |
| SLC28A3 | ENSG00000197506 | 0.00 | 0.00 | 0 | 0 |
| CLCN4 | ENSG00000073464 | 0.00 | 0.00 | 0 | 0 |
| PTPRK | ENSG00000152894 | 0.00 | 0.13 | 0 | 1 |
| SLC27A4 | ENSG00000167114 | 0.00 | 0.11 | 0 | 1 |
| GMPR | ENSG00000137198 | 0.00 | 0.00 | 0 | 0 |
| DNAJA1 | ENSG00000086061 | 0.00 | 0.00 | 0 | 0 |
| ICAM1 | ENSG00000090339 | 0.00 | 0.00 | 0 | 0 |
| SIDT2 | ENSG00000149577 | 0.00 | 1.05 | 0 | 5 |
| PRELP | ENSG00000188783 | 0.00 | 0.00 | 0 | 0 |
| FGF10 | ENSG00000070193 | 0.00 | 0.00 | 0 | 0 |
| ADGRL1 | ENSG00000072071 | 0.00 | 0.00 | 0 | 0 |
| PRIMPOL | ENSG00000164306 | 0.00 | 1.41 | 0 | 9 |
| SLCO3A1 | ENSG00000176463 | 0.18 | 0.00 | 1 | 0 |
| MBD5 | ENSG00000204406 | 0.00 | 0.30 | 0 | 2 |
| PTPDC1 | ENSG00000158079 | 0.00 | 0.00 | 0 | 0 |
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