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 |
| HCN3 | ENSG00000143630 | 0.76 | 0.00 | 4 | 0 |
| MLK4 | ENSG00000143674 | 0.25 | 0.10 | 1 | 1 |
| ACP1 | ENSG00000143727 | 0.16 | 0.39 | 1 | 2 |
| LEFTY2 | ENSG00000143768 | 0.00 | 0.00 | 0 | 0 |
| PSEN2 | ENSG00000143801 | 0.00 | 0.25 | 0 | 1 |
| WNT9A | ENSG00000143816 | 0.00 | 0.00 | 0 | 0 |
| REN | ENSG00000143839 | 0.00 | 0.00 | 0 | 0 |
| PTPN7 | ENSG00000143851 | 0.00 | 0.00 | 0 | 0 |
| GDF7 | ENSG00000143869 | 0.00 | 0.00 | 0 | 0 |
| CALM2 | ENSG00000143933 | 0.12 | 0.00 | 1 | 0 |
| ASXL2 | ENSG00000143970 | 0.00 | 0.00 | 0 | 0 |
| DUSP11 | ENSG00000144048 | 0.00 | 0.00 | 0 | 0 |
| THNSL2 | ENSG00000144115 | 0.00 | 0.00 | 0 | 0 |
| C1QL2 | ENSG00000144119 | 0.00 | 0.00 | 0 | 0 |
| FBLN7 | ENSG00000144152 | 0.00 | 0.00 | 0 | 0 |
| CNGA3 | ENSG00000144191 | 0.00 | 0.00 | 0 | 0 |
| LYG1 | ENSG00000144214 | 0.00 | 0.00 | 0 | 0 |
| GPR17 | ENSG00000144230 | 0.00 | 0.00 | 0 | 0 |
| SCN1A | ENSG00000144285 | 0.00 | 0.00 | 0 | 0 |
| METTL21A | ENSG00000144401 | 0.00 | 0.00 | 0 | 0 |
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