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 |
| CHGA | ENSG00000100604 | 0.00 | 0.00 | 0 | 0 |
| SLC10A1 | ENSG00000100652 | 0.00 | 0.00 | 0 | 0 |
| SERPINA4 | ENSG00000100665 | 0.00 | 0.00 | 0 | 0 |
| BDKRB1 | ENSG00000100739 | 0.00 | 0.00 | 0 | 0 |
| PSMC1 | ENSG00000100764 | 0.00 | 0.40 | 0 | 1 |
| PSMB5 | ENSG00000100804 | 0.29 | 0.00 | 1 | 0 |
| APEX1 | ENSG00000100823 | 0.00 | 0.10 | 0 | 1 |
| NFKBIA | ENSG00000100906 | 0.24 | 0.00 | 1 | 0 |
| GMPR2 | ENSG00000100938 | 0.00 | 0.00 | 0 | 0 |
| GSS | ENSG00000100983 | 0.00 | 0.00 | 0 | 0 |
| PROCR | ENSG00000101000 | 0.00 | 0.00 | 0 | 0 |
| R3HDML | ENSG00000101074 | 0.00 | 0.00 | 0 | 0 |
| BMP7 | ENSG00000101144 | 0.00 | 0.00 | 0 | 0 |
| CTSZ | ENSG00000101160 | 0.00 | 0.00 | 0 | 0 |
| TUBB1 | ENSG00000101162 | 0.00 | 0.00 | 0 | 0 |
| HRH3 | ENSG00000101180 | 0.00 | 0.00 | 0 | 0 |
| AVP | ENSG00000101200 | 0.00 | 0.00 | 0 | 0 |
| COL20A1 | ENSG00000101203 | 0.00 | 0.00 | 0 | 0 |
| CHRNA4 | ENSG00000101204 | 0.00 | 0.00 | 0 | 0 |
| PTK6 | ENSG00000101213 | 0.13 | 0.00 | 1 | 0 |
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