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 |
| TNFRSF11B | ENSG00000164761 | 0.00 | 0.00 | 0 | 0 |
| INHA | ENSG00000123999 | 0.00 | 0.19 | 0 | 1 |
| PKDCC | ENSG00000162878 | 0.17 | 0.00 | 1 | 0 |
| GGT6 | ENSG00000167741 | 0.00 | 0.00 | 0 | 0 |
| MAP2K4 | ENSG00000065559 | 0.67 | 0.77 | 1 | 5 |
| EPHA1 | ENSG00000146904 | 0.11 | 0.00 | 1 | 0 |
| PTPRM | ENSG00000173482 | 0.00 | 0.00 | 0 | 0 |
| KCNK7 | ENSG00000173338 | 0.00 | 0.00 | 0 | 0 |
| TCN1 | ENSG00000134827 | 0.00 | 0.00 | 0 | 0 |
| BAZ2B | ENSG00000123636 | 0.00 | 0.00 | 0 | 0 |
| F2R | ENSG00000181104 | 0.00 | 0.70 | 0 | 1 |
| SLC12A2 | ENSG00000064651 | 0.00 | 0.13 | 0 | 1 |
| RTN3 | ENSG00000133318 | 0.12 | 0.12 | 1 | 1 |
| SIRT7 | ENSG00000187531 | 0.63 | 0.00 | 3 | 0 |
| SCUBE3 | ENSG00000146197 | 0.00 | 0.00 | 0 | 0 |
| CAPN9 | ENSG00000135773 | 0.25 | 0.00 | 1 | 0 |
| HSD11B1 | ENSG00000117594 | 0.00 | 0.00 | 0 | 0 |
| FCER1A | ENSG00000179639 | 0.00 | 0.00 | 0 | 0 |
| DPP4 | ENSG00000197635 | 0.00 | 0.00 | 0 | 0 |
| CRB1 | ENSG00000134376 | 0.00 | 0.00 | 0 | 0 |
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