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 |
| OR51F1 | ENSG00000280021 | 0.00 | 0.00 | 0 | 0 |
| OR8B4 | ENSG00000280090 | 0.00 | 0.00 | 0 | 0 |
| OR1B1 | ENSG00000280094 | 0.00 | 0.00 | 0 | 0 |
| OR1S1 | ENSG00000280204 | 0.00 | 0.00 | 0 | 0 |
| OR12D2 | ENSG00000280236 | 0.00 | 0.00 | 0 | 0 |
| OR8K3 | ENSG00000280314 | 0.00 | 0.00 | 0 | 0 |
| EGFR | ENSG00000146648 | 3.05 | 0.00 | 7 | 0 |
| FLT3 | ENSG00000122025 | 0.00 | 0.00 | 0 | 0 |
| TTK | ENSG00000112742 | 0.00 | 0.16 | 0 | 1 |
| BUB1B | ENSG00000156970 | 0.00 | 0.69 | 0 | 2 |
| MET | ENSG00000105976 | 0.52 | 0.00 | 3 | 0 |
| TOP2A | ENSG00000131747 | 0.00 | 0.00 | 0 | 0 |
| FGFR2 | ENSG00000066468 | 0.29 | 0.19 | 1 | 1 |
| FGFR3 | ENSG00000068078 | 1.56 | 0.00 | 3 | 0 |
| FGF19 | ENSG00000162344 | 2.77 | 0.00 | 1 | 0 |
| ERBB2 | ENSG00000141736 | 5.86 | 0.00 | 11 | 0 |
| BCL2 | ENSG00000171791 | 0.20 | 0.53 | 1 | 4 |
| RRM2 | ENSG00000171848 | 0.15 | 0.16 | 1 | 1 |
| CDK6 | ENSG00000105810 | 2.03 | 0.00 | 5 | 0 |
| BRAF | ENSG00000157764 | 0.36 | 0.14 | 2 | 1 |
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