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 |
| NRG3 | ENSG00000185737 | 0.00 | 0.00 | 0 | 0 |
| TKT | ENSG00000163931 | 0.00 | 0.52 | 0 | 3 |
| BAP1 | ENSG00000163930 | 0.00 | 1.49 | 0 | 5 |
| BIRC7 | ENSG00000101197 | 0.11 | 0.00 | 1 | 0 |
| COL24A1 | ENSG00000171502 | 0.00 | 0.11 | 0 | 1 |
| DPP10 | ENSG00000175497 | 0.00 | 0.00 | 0 | 0 |
| ZMYND11 | ENSG00000015171 | 0.00 | 0.83 | 0 | 4 |
| TOP1 | ENSG00000198900 | 0.00 | 0.00 | 0 | 0 |
| NT5E | ENSG00000135318 | 0.00 | 0.10 | 0 | 1 |
| BMP2K | ENSG00000138756 | 0.00 | 0.00 | 0 | 0 |
| TYMP | ENSG00000025708 | 0.00 | 1.07 | 0 | 4 |
| CPAMD8 | ENSG00000160111 | 0.00 | 0.00 | 0 | 0 |
| PTPN13 | ENSG00000163629 | 0.00 | 0.00 | 0 | 0 |
| AKT3 | ENSG00000117020 | 0.15 | 0.22 | 1 | 1 |
| CD101 | ENSG00000134256 | 0.00 | 0.35 | 0 | 2 |
| F10 | ENSG00000126218 | 0.80 | 0.00 | 4 | 0 |
| TP73 | ENSG00000078900 | 0.00 | 0.22 | 0 | 2 |
| NR3C2 | ENSG00000151623 | 0.00 | 0.00 | 0 | 0 |
| EP300 | ENSG00000100393 | 0.33 | 0.00 | 1 | 0 |
| MAP3K8 | ENSG00000107968 | 0.00 | 0.00 | 0 | 0 |
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