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 |
| COMP | ENSG00000105664 | 0.00 | 0.00 | 0 | 0 |
| GAPDHS | ENSG00000105679 | 0.00 | 0.00 | 0 | 0 |
| MAG | ENSG00000105695 | 0.00 | 0.00 | 0 | 0 |
| HAMP | ENSG00000105697 | 0.00 | 0.00 | 0 | 0 |
| SCN1B | ENSG00000105711 | 0.00 | 0.00 | 0 | 0 |
| TFPI2 | ENSG00000105825 | 0.25 | 0.00 | 1 | 0 |
| NAMPT | ENSG00000105835 | 0.00 | 0.00 | 0 | 0 |
| PIK3CG | ENSG00000105851 | 0.00 | 0.00 | 0 | 0 |
| PON3 | ENSG00000105852 | 0.00 | 0.00 | 0 | 0 |
| PON2 | ENSG00000105854 | 0.00 | 0.00 | 0 | 0 |
| ITGB8 | ENSG00000105855 | 0.13 | 0.00 | 1 | 0 |
| NPVF | ENSG00000105954 | 0.00 | 0.00 | 0 | 0 |
| FKBP14 | ENSG00000106080 | 0.00 | 0.00 | 0 | 0 |
| STX1A | ENSG00000106089 | 0.12 | 0.00 | 1 | 0 |
| NOD1 | ENSG00000106100 | 0.00 | 0.00 | 0 | 0 |
| EPHB6 | ENSG00000106123 | 0.00 | 0.00 | 0 | 0 |
| GHRHR | ENSG00000106128 | 0.00 | 0.00 | 0 | 0 |
| CASP2 | ENSG00000106144 | 0.32 | 0.14 | 2 | 1 |
| CCL24 | ENSG00000106178 | 0.00 | 0.00 | 0 | 0 |
| NPTX2 | ENSG00000106236 | 0.00 | 0.00 | 0 | 0 |
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