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 |
| CDYL | ENSG00000153046 | 0.67 | 0.38 | 3 | 2 |
| CLCN5 | ENSG00000171365 | 0.00 | 0.00 | 0 | 0 |
| CDKL2 | ENSG00000138769 | 0.00 | 0.00 | 0 | 0 |
| KCNJ3 | ENSG00000162989 | 0.00 | 0.00 | 0 | 0 |
| CACHD1 | ENSG00000158966 | 0.00 | 0.00 | 0 | 0 |
| HABP2 | ENSG00000148702 | 0.00 | 0.00 | 0 | 0 |
| A2ML1 | ENSG00000166535 | 0.00 | 0.00 | 0 | 0 |
| DUSP16 | ENSG00000111266 | 0.00 | 0.17 | 0 | 1 |
| ITPKC | ENSG00000086544 | 0.00 | 0.11 | 0 | 1 |
| CRLF1 | ENSG00000006016 | 0.00 | 0.00 | 0 | 0 |
| ITGAM | ENSG00000169896 | 0.00 | 0.00 | 0 | 0 |
| PTPN6 | ENSG00000111679 | 0.00 | 0.00 | 0 | 0 |
| NEK8 | ENSG00000160602 | 0.00 | 0.00 | 0 | 0 |
| SLC22A9 | ENSG00000149742 | 0.00 | 0.00 | 0 | 0 |
| IL17RE | ENSG00000163701 | 0.00 | 0.00 | 0 | 0 |
| IGFBP2 | ENSG00000115457 | 0.00 | 0.34 | 0 | 1 |
| BBOX1 | ENSG00000129151 | 0.00 | 0.00 | 0 | 0 |
| PKHD1 | ENSG00000170927 | 0.00 | 0.00 | 0 | 0 |
| NCOA1 | ENSG00000084676 | 0.00 | 0.12 | 0 | 1 |
| ACRBP | ENSG00000111644 | 0.00 | 0.00 | 0 | 0 |
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