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 |
| PSMB11 | ENSG00000222028 | 0.00 | 0.00 | 0 | 0 |
| HLA-DPB1 | ENSG00000223865 | 0.00 | 0.00 | 0 | 0 |
| C1QTNF5 | ENSG00000223953 | 0.00 | 0.24 | 0 | 1 |
| C4B | ENSG00000224389 | 0.00 | 0.00 | 0 | 0 |
| HSP90AA2P | ENSG00000224411 | 0.00 | 0.00 | 0 | 0 |
| GPX5 | ENSG00000224586 | 0.00 | 0.00 | 0 | 0 |
| OR6V1 | ENSG00000225781 | 0.00 | 0.00 | 0 | 0 |
| OR52I2 | ENSG00000226288 | 0.00 | 0.00 | 0 | 0 |
| NPY6R | ENSG00000226306 | 0.28 | 0.00 | 1 | 0 |
| TAS2R46 | ENSG00000226761 | 0.00 | 0.00 | 0 | 0 |
| LTA | ENSG00000226979 | 0.00 | 0.00 | 0 | 0 |
| LTB | ENSG00000227507 | 0.00 | 0.00 | 0 | 0 |
| IFNA14 | ENSG00000228083 | 0.00 | 0.00 | 0 | 0 |
| OR2M3 | ENSG00000228198 | 0.00 | 0.00 | 0 | 0 |
| MT-ATP8 | ENSG00000228253 | 0.00 | 0.00 | 0 | 0 |
| VN1R4 | ENSG00000228567 | 0.00 | 0.00 | 0 | 0 |
| DHFR | ENSG00000228716 | 0.00 | 0.67 | 0 | 1 |
| PGA4 | ENSG00000229183 | 0.00 | 0.00 | 0 | 0 |
| ORM1 | ENSG00000229314 | 0.00 | 0.00 | 0 | 0 |
| SPINK8 | ENSG00000229453 | 0.00 | 0.16 | 0 | 1 |
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