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 |
| TET1 | ENSG00000138336 | 0.00 | 0.00 | 0 | 0 |
| MAP2K6 | ENSG00000108984 | 0.87 | 0.00 | 4 | 0 |
| NUAK2 | ENSG00000163545 | 0.00 | 0.00 | 0 | 0 |
| MAPK12 | ENSG00000188130 | 0.00 | 1.02 | 0 | 4 |
| SLC35A1 | ENSG00000164414 | 0.00 | 0.44 | 0 | 3 |
| PTPRH | ENSG00000080031 | 0.17 | 0.00 | 1 | 0 |
| NEK11 | ENSG00000114670 | 0.00 | 0.00 | 0 | 0 |
| SLC13A5 | ENSG00000141485 | 0.00 | 0.00 | 0 | 0 |
| CBX7 | ENSG00000100307 | 0.00 | 0.00 | 0 | 0 |
| FAP | ENSG00000078098 | 0.00 | 0.00 | 0 | 0 |
| CELSR1 | ENSG00000075275 | 0.00 | 0.11 | 0 | 1 |
| TGM5 | ENSG00000104055 | 0.00 | 0.00 | 0 | 0 |
| ATP1A3 | ENSG00000105409 | 0.00 | 0.00 | 0 | 0 |
| RYR2 | ENSG00000198626 | 0.00 | 0.00 | 0 | 0 |
| BLK | ENSG00000136573 | 0.53 | 0.00 | 1 | 0 |
| ADGRG6 | ENSG00000112414 | 0.00 | 0.14 | 0 | 1 |
| NTM | ENSG00000182667 | 0.00 | 0.00 | 0 | 0 |
| TNR | ENSG00000116147 | 0.00 | 0.00 | 0 | 0 |
| TAF1 | ENSG00000147133 | 0.00 | 0.00 | 0 | 0 |
| FBN2 | ENSG00000138829 | 0.00 | 0.00 | 0 | 0 |
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