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 |
| ICAM2 | ENSG00000108622 | 0.00 | 0.00 | 0 | 0 |
| FBN1 | ENSG00000166147 | 0.00 | 0.00 | 0 | 0 |
| FCRLA | ENSG00000132185 | 0.00 | 0.00 | 0 | 0 |
| PYGL | ENSG00000100504 | 0.00 | 0.00 | 0 | 0 |
| CNGB1 | ENSG00000070729 | 0.00 | 0.00 | 0 | 0 |
| MCOLN2 | ENSG00000153898 | 0.00 | 0.00 | 0 | 0 |
| ACTN4 | ENSG00000130402 | 0.55 | 0.11 | 1 | 1 |
| ZCWPW1 | ENSG00000078487 | 0.00 | 0.00 | 0 | 0 |
| SSH3 | ENSG00000172830 | 0.53 | 0.00 | 2 | 0 |
| NR1H3 | ENSG00000025434 | 0.00 | 0.00 | 0 | 0 |
| CPB2 | ENSG00000080618 | 0.00 | 0.00 | 0 | 0 |
| RORA | ENSG00000069667 | 0.00 | 0.00 | 0 | 0 |
| DPF3 | ENSG00000205683 | 0.00 | 0.11 | 0 | 1 |
| OBSCN | ENSG00000154358 | 0.14 | 0.23 | 1 | 1 |
| PTK2B | ENSG00000120899 | 0.00 | 0.51 | 0 | 4 |
| CYP46A1 | ENSG00000036530 | 0.00 | 0.00 | 0 | 0 |
| PLCB3 | ENSG00000149782 | 0.11 | 0.00 | 1 | 0 |
| NRXN3 | ENSG00000021645 | 0.00 | 0.22 | 0 | 2 |
| CERK | ENSG00000100422 | 0.00 | 0.64 | 0 | 4 |
| KCNC4 | ENSG00000116396 | 0.00 | 0.23 | 0 | 2 |
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