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 |
| HPD | ENSG00000158104 | 0.00 | 0.00 | 0 | 0 |
| CES4A | ENSG00000172824 | 0.15 | 0.00 | 1 | 0 |
| TOP2B | ENSG00000077097 | 0.00 | 0.18 | 0 | 1 |
| SLC9A3 | ENSG00000066230 | 0.18 | 0.00 | 1 | 0 |
| PTAFR | ENSG00000169403 | 0.00 | 0.00 | 0 | 0 |
| EWSR1 | ENSG00000182944 | 0.23 | 0.00 | 1 | 0 |
| CHST4 | ENSG00000140835 | 0.00 | 0.00 | 0 | 0 |
| NME9 | ENSG00000181322 | 0.00 | 0.00 | 0 | 0 |
| GSR | ENSG00000104687 | 0.00 | 0.11 | 0 | 1 |
| EMILIN2 | ENSG00000132205 | 0.00 | 0.00 | 0 | 0 |
| DYRK1B | ENSG00000105204 | 0.73 | 0.11 | 1 | 1 |
| CD300E | ENSG00000186407 | 0.00 | 0.00 | 0 | 0 |
| PDE4C | ENSG00000105650 | 0.00 | 0.00 | 0 | 0 |
| PDE4B | ENSG00000184588 | 0.00 | 0.00 | 0 | 0 |
| GRIN1 | ENSG00000176884 | 0.17 | 0.00 | 1 | 0 |
| LTK | ENSG00000062524 | 0.00 | 0.19 | 0 | 1 |
| ADGRF4 | ENSG00000153294 | 0.00 | 0.00 | 0 | 0 |
| SLC16A14 | ENSG00000163053 | 0.00 | 0.36 | 0 | 1 |
| DMBT1 | ENSG00000187908 | 0.00 | 0.00 | 0 | 0 |
| GAN | ENSG00000261609 | 0.00 | 0.24 | 0 | 1 |
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