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 |
| AGBL3 | ENSG00000146856 | 0.11 | 0.16 | 1 | 1 |
| PADI1 | ENSG00000142623 | 0.00 | 0.00 | 0 | 0 |
| HDAC1 | ENSG00000116478 | 0.00 | 0.00 | 0 | 0 |
| GDF3 | ENSG00000184344 | 0.57 | 0.00 | 1 | 0 |
| GTF3C4 | ENSG00000125484 | 0.00 | 0.39 | 0 | 2 |
| STAT5A | ENSG00000126561 | 0.00 | 0.00 | 0 | 0 |
| SLC16A1 | ENSG00000155380 | 0.00 | 0.29 | 0 | 2 |
| PRLR | ENSG00000113494 | 0.00 | 0.00 | 0 | 0 |
| PAEP | ENSG00000122133 | 0.00 | 0.24 | 0 | 1 |
| SETDB1 | ENSG00000143379 | 3.07 | 0.00 | 11 | 0 |
| GABRD | ENSG00000187730 | 0.00 | 0.28 | 0 | 1 |
| PPME1 | ENSG00000214517 | 0.49 | 0.10 | 1 | 1 |
| CD70 | ENSG00000125726 | 0.00 | 0.00 | 0 | 0 |
| PRKCZ | ENSG00000067606 | 0.00 | 1.07 | 0 | 6 |
| ATP1B2 | ENSG00000129244 | 0.00 | 1.12 | 0 | 3 |
| KRT19 | ENSG00000171345 | 0.00 | 0.00 | 0 | 0 |
| RXRA | ENSG00000186350 | 0.00 | 0.25 | 0 | 1 |
| TNFRSF19 | ENSG00000127863 | 0.00 | 0.00 | 0 | 0 |
| PRKAR1A | ENSG00000108946 | 0.87 | 0.00 | 4 | 0 |
| STK33 | ENSG00000130413 | 0.00 | 0.00 | 0 | 0 |
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