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 |
| ATP1B3 | ENSG00000069849 | 0.00 | 0.00 | 0 | 0 |
| PMPCB | ENSG00000105819 | 0.00 | 0.00 | 0 | 0 |
| STK25 | ENSG00000115694 | 0.00 | 2.49 | 0 | 10 |
| COL3A1 | ENSG00000168542 | 0.00 | 0.00 | 0 | 0 |
| F2 | ENSG00000180210 | 0.00 | 0.00 | 0 | 0 |
| SEMA3A | ENSG00000075213 | 0.00 | 0.00 | 0 | 0 |
| CPT1B | ENSG00000205560 | 0.00 | 0.92 | 0 | 3 |
| PRDM16 | ENSG00000142611 | 0.00 | 0.00 | 0 | 0 |
| FMO5 | ENSG00000131781 | 0.00 | 0.00 | 0 | 0 |
| LY9 | ENSG00000122224 | 0.00 | 0.00 | 0 | 0 |
| DKK3 | ENSG00000050165 | 0.00 | 0.00 | 0 | 0 |
| P2RY13 | ENSG00000181631 | 0.00 | 0.00 | 0 | 0 |
| MBOAT7 | ENSG00000125505 | 0.17 | 0.29 | 1 | 2 |
| ADAMTS5 | ENSG00000154736 | 0.00 | 0.00 | 0 | 0 |
| JMJD6 | ENSG00000070495 | 0.85 | 0.00 | 4 | 0 |
| PRSS23 | ENSG00000150687 | 0.00 | 0.00 | 0 | 0 |
| TSHR | ENSG00000165409 | 0.00 | 0.11 | 0 | 1 |
| EDIL3 | ENSG00000164176 | 0.00 | 0.00 | 0 | 0 |
| SEMA4B | ENSG00000185033 | 0.77 | 0.00 | 4 | 0 |
| SLC27A2 | ENSG00000140284 | 0.00 | 0.00 | 0 | 0 |
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