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 |
| MTA3 | ENSG00000057935 | 0.00 | 0.00 | 0 | 0 |
| TRIM4 | ENSG00000146833 | 0.00 | 0.00 | 0 | 0 |
| STK39 | ENSG00000198648 | 0.00 | 0.00 | 0 | 0 |
| AGA | ENSG00000038002 | 0.00 | 0.56 | 0 | 4 |
| NR2F6 | ENSG00000160113 | 0.00 | 0.00 | 0 | 0 |
| ERBB2IP | ENSG00000112851 | 0.00 | 0.00 | 0 | 0 |
| IRAK4 | ENSG00000198001 | 0.00 | 0.00 | 0 | 0 |
| TDRD9 | ENSG00000156414 | 0.00 | 0.00 | 0 | 0 |
| CST3 | ENSG00000101439 | 0.00 | 0.00 | 0 | 0 |
| ABHD12 | ENSG00000100997 | 0.00 | 0.00 | 0 | 0 |
| LNPEP | ENSG00000113441 | 0.00 | 0.12 | 0 | 1 |
| RYR3 | ENSG00000198838 | 0.00 | 0.00 | 0 | 0 |
| ATP2B4 | ENSG00000058668 | 0.00 | 0.00 | 0 | 0 |
| MAN2A1 | ENSG00000112893 | 0.00 | 0.14 | 0 | 1 |
| VWC2 | ENSG00000188730 | 0.00 | 0.00 | 0 | 0 |
| GABRA5 | ENSG00000186297 | 0.00 | 0.00 | 0 | 0 |
| PAPPA2 | ENSG00000116183 | 0.00 | 0.00 | 0 | 0 |
| PLSCR1 | ENSG00000188313 | 0.00 | 0.00 | 0 | 0 |
| MAPK9 | ENSG00000050748 | 0.33 | 0.00 | 1 | 0 |
| GRIN3B | ENSG00000116032 | 0.00 | 0.00 | 0 | 0 |
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