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 |
| JAM2 | ENSG00000154721 | 0.00 | 0.00 | 0 | 0 |
| PTGFRN | ENSG00000134247 | 0.00 | 0.49 | 0 | 3 |
| RERE | ENSG00000142599 | 0.00 | 1.96 | 0 | 6 |
| AURKC | ENSG00000105146 | 0.35 | 0.18 | 2 | 1 |
| HTRA3 | ENSG00000170801 | 0.00 | 0.00 | 0 | 0 |
| ALDH3B2 | ENSG00000132746 | 0.00 | 0.00 | 0 | 0 |
| ADCY1 | ENSG00000164742 | 0.00 | 0.00 | 0 | 0 |
| PRDM11 | ENSG00000019485 | 0.12 | 0.00 | 1 | 0 |
| ARSB | ENSG00000113273 | 0.00 | 0.67 | 0 | 1 |
| VIPR2 | ENSG00000106018 | 0.00 | 0.00 | 0 | 0 |
| SLC30A4 | ENSG00000104154 | 0.00 | 0.14 | 0 | 1 |
| RPS6KA2 | ENSG00000071242 | 0.00 | 0.61 | 0 | 2 |
| SLC15A1 | ENSG00000088386 | 0.53 | 0.00 | 3 | 0 |
| SLC3A2 | ENSG00000168003 | 0.00 | 0.00 | 0 | 0 |
| PTPRT | ENSG00000196090 | 0.00 | 0.00 | 0 | 0 |
| CYP2J2 | ENSG00000134716 | 0.00 | 0.00 | 0 | 0 |
| WWOX | ENSG00000186153 | 0.00 | 2.78 | 0 | 14 |
| IRAK2 | ENSG00000134070 | 0.00 | 0.00 | 0 | 0 |
| TWF2 | ENSG00000247596 | 0.00 | 0.70 | 0 | 4 |
| COL8A1 | ENSG00000144810 | 0.00 | 0.00 | 0 | 0 |
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