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 |
| PHRF1 | ENSG00000070047 | 0.00 | 1.25 | 0 | 6 |
| LRIG3 | ENSG00000139263 | 0.00 | 0.00 | 0 | 0 |
| EGFL6 | ENSG00000198759 | 0.00 | 0.00 | 0 | 0 |
| TGFB1 | ENSG00000105329 | 0.00 | 0.00 | 0 | 0 |
| MBTD1 | ENSG00000011258 | 0.00 | 0.00 | 0 | 0 |
| ADCK2 | ENSG00000133597 | 0.36 | 0.14 | 2 | 1 |
| INPP5K | ENSG00000132376 | 0.00 | 0.14 | 0 | 1 |
| SENP7 | ENSG00000138468 | 0.00 | 0.00 | 0 | 0 |
| SOAT1 | ENSG00000057252 | 0.00 | 0.00 | 0 | 0 |
| POR | ENSG00000127948 | 0.00 | 0.00 | 0 | 0 |
| EMC10 | ENSG00000161671 | 0.23 | 0.45 | 1 | 2 |
| CSNK1E | ENSG00000213923 | 0.00 | 0.00 | 0 | 0 |
| ZRANB2 | ENSG00000132485 | 0.00 | 0.00 | 0 | 0 |
| CHD8 | ENSG00000100888 | 0.29 | 0.00 | 1 | 0 |
| NLGN4X | ENSG00000146938 | 0.00 | 0.00 | 0 | 0 |
| PGGT1B | ENSG00000164219 | 0.21 | 0.13 | 1 | 1 |
| CDK13 | ENSG00000065883 | 0.00 | 0.00 | 0 | 0 |
| ING1 | ENSG00000153487 | 1.04 | 0.00 | 6 | 0 |
| ITGB2 | ENSG00000160255 | 0.00 | 0.00 | 0 | 0 |
| PHF21B | ENSG00000056487 | 0.00 | 0.00 | 0 | 0 |
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