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 |
| P2RY2 | ENSG00000175591 | 0.00 | 0.00 | 0 | 0 |
| ABCA12 | ENSG00000144452 | 0.00 | 0.00 | 0 | 0 |
| CHEK2 | ENSG00000183765 | 0.00 | 0.00 | 0 | 0 |
| FGL1 | ENSG00000104760 | 0.00 | 0.31 | 0 | 2 |
| SLC7A8 | ENSG00000092068 | 0.00 | 0.00 | 0 | 0 |
| IL13RA1 | ENSG00000131724 | 0.00 | 0.00 | 0 | 0 |
| PGR | ENSG00000082175 | 0.00 | 0.00 | 0 | 0 |
| KCNH2 | ENSG00000055118 | 0.10 | 0.00 | 1 | 0 |
| KDM3A | ENSG00000115548 | 0.23 | 0.00 | 1 | 0 |
| FUT2 | ENSG00000176920 | 0.21 | 0.34 | 1 | 1 |
| TNK2 | ENSG00000061938 | 0.55 | 0.14 | 2 | 1 |
| KLHL8 | ENSG00000145332 | 0.00 | 0.11 | 0 | 1 |
| CACNG2 | ENSG00000166862 | 0.00 | 0.00 | 0 | 0 |
| LAMA1 | ENSG00000101680 | 0.00 | 0.00 | 0 | 0 |
| WNT7A | ENSG00000154764 | 0.00 | 0.00 | 0 | 0 |
| ADRBK1 | ENSG00000173020 | 0.52 | 0.00 | 2 | 0 |
| SLC6A2 | ENSG00000103546 | 0.00 | 0.00 | 0 | 0 |
| MAPT | ENSG00000186868 | 0.00 | 0.00 | 0 | 0 |
| DPEP1 | ENSG00000015413 | 0.00 | 0.11 | 0 | 1 |
| TMPRSS6 | ENSG00000187045 | 0.00 | 0.00 | 0 | 0 |
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