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 |
| EPHB3 | ENSG00000182580 | 0.39 | 0.00 | 2 | 0 |
| ADCY2 | ENSG00000078295 | 0.00 | 0.00 | 0 | 0 |
| ARID4B | ENSG00000054267 | 1.14 | 0.24 | 4 | 1 |
| PYGO2 | ENSG00000163348 | 1.47 | 0.00 | 6 | 0 |
| PLP1 | ENSG00000123560 | 0.00 | 0.00 | 0 | 0 |
| EMILIN3 | ENSG00000183798 | 0.00 | 0.00 | 0 | 0 |
| PTPRC | ENSG00000081237 | 0.00 | 0.00 | 0 | 0 |
| SLC25A24 | ENSG00000085491 | 0.00 | 0.23 | 0 | 2 |
| ADGRA2 | ENSG00000020181 | 0.00 | 0.00 | 0 | 0 |
| QSOX2 | ENSG00000165661 | 0.00 | 0.22 | 0 | 1 |
| SHPRH | ENSG00000146414 | 0.00 | 0.43 | 0 | 3 |
| G6PD | ENSG00000160211 | 0.79 | 0.00 | 4 | 0 |
| SGK1 | ENSG00000118515 | 0.00 | 0.24 | 0 | 2 |
| ANPEP | ENSG00000166825 | 0.00 | 0.00 | 0 | 0 |
| GABRG3 | ENSG00000182256 | 0.00 | 0.00 | 0 | 0 |
| ABCA4 | ENSG00000198691 | 0.00 | 0.11 | 0 | 1 |
| HS3ST1 | ENSG00000002587 | 0.00 | 0.00 | 0 | 0 |
| ARSG | ENSG00000141337 | 0.45 | 0.00 | 2 | 0 |
| PDE1C | ENSG00000154678 | 0.00 | 0.00 | 0 | 0 |
| MAPK10 | ENSG00000109339 | 0.00 | 0.00 | 0 | 0 |
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