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 |
| LRP1 | ENSG00000123384 | 0.00 | 0.00 | 0 | 0 |
| AHR | ENSG00000106546 | 0.43 | 0.00 | 2 | 0 |
| MATK | ENSG00000007264 | 0.00 | 0.00 | 0 | 0 |
| PVRL2 | ENSG00000130202 | 0.24 | 0.46 | 1 | 2 |
| CR1L | ENSG00000197721 | 0.00 | 0.00 | 0 | 0 |
| KDM1B | ENSG00000165097 | 0.00 | 0.29 | 0 | 2 |
| ADAMTS13 | ENSG00000160323 | 0.00 | 0.25 | 0 | 1 |
| HSPB1 | ENSG00000106211 | 0.00 | 0.00 | 0 | 0 |
| MAP3K12 | ENSG00000139625 | 0.00 | 0.00 | 0 | 0 |
| CEACAM7 | ENSG00000007306 | 0.00 | 0.00 | 0 | 0 |
| VWA2 | ENSG00000165816 | 0.00 | 0.00 | 0 | 0 |
| LPAR3 | ENSG00000171517 | 0.00 | 0.00 | 0 | 0 |
| HPRT1 | ENSG00000165704 | 0.15 | 0.00 | 1 | 0 |
| STK24 | ENSG00000102572 | 0.70 | 0.00 | 4 | 0 |
| ABCC8 | ENSG00000006071 | 0.00 | 0.00 | 0 | 0 |
| SLC29A2 | ENSG00000174669 | 0.00 | 0.00 | 0 | 0 |
| HTR7 | ENSG00000148680 | 0.00 | 0.00 | 0 | 0 |
| FAS | ENSG00000026103 | 0.00 | 0.31 | 0 | 1 |
| BRWD3 | ENSG00000165288 | 0.00 | 0.00 | 0 | 0 |
| FGA | ENSG00000171560 | 0.00 | 0.00 | 0 | 0 |
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