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 |
| HERC1 | ENSG00000103657 | 0.00 | 0.00 | 0 | 0 |
| IGSF11 | ENSG00000144847 | 0.00 | 0.00 | 0 | 0 |
| SCML2 | ENSG00000102098 | 0.00 | 0.00 | 0 | 0 |
| GRID1 | ENSG00000182771 | 0.00 | 0.00 | 0 | 0 |
| NRG1 | ENSG00000157168 | 0.00 | 0.00 | 0 | 0 |
| CACNB2 | ENSG00000165995 | 0.00 | 0.00 | 0 | 0 |
| CCNA1 | ENSG00000133101 | 0.00 | 0.00 | 0 | 0 |
| PTK7 | ENSG00000112655 | 0.00 | 0.00 | 0 | 0 |
| TNK1 | ENSG00000174292 | 0.00 | 0.15 | 0 | 1 |
| ADCY7 | ENSG00000121281 | 0.00 | 0.00 | 0 | 0 |
| TGFBR2 | ENSG00000163513 | 0.00 | 0.00 | 0 | 0 |
| IRAK3 | ENSG00000090376 | 0.00 | 0.00 | 0 | 0 |
| HDAC9 | ENSG00000048052 | 0.11 | 0.00 | 1 | 0 |
| ADCY4 | ENSG00000129467 | 0.00 | 0.00 | 0 | 0 |
| EDNRA | ENSG00000151617 | 0.00 | 0.00 | 0 | 0 |
| SLC7A10 | ENSG00000130876 | 0.00 | 0.00 | 0 | 0 |
| SLC9A1 | ENSG00000090020 | 0.00 | 1.18 | 0 | 5 |
| KDM2B | ENSG00000089094 | 0.00 | 0.23 | 0 | 1 |
| ADRBK2 | ENSG00000100077 | 0.00 | 0.00 | 0 | 0 |
| SSR2 | ENSG00000163479 | 2.56 | 0.00 | 7 | 0 |
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