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 |
| MMP19 | ENSG00000123342 | 0.00 | 0.00 | 0 | 0 |
| FSTL5 | ENSG00000168843 | 0.00 | 0.00 | 0 | 0 |
| PPP5C | ENSG00000011485 | 0.13 | 0.51 | 1 | 2 |
| CYP4F12 | ENSG00000186204 | 0.00 | 0.00 | 0 | 0 |
| AKR1E2 | ENSG00000165568 | 0.18 | 0.00 | 1 | 0 |
| PDE9A | ENSG00000160191 | 0.00 | 0.00 | 0 | 0 |
| PLBD2 | ENSG00000151176 | 0.00 | 0.22 | 0 | 1 |
| PLCL2 | ENSG00000154822 | 0.00 | 0.00 | 0 | 0 |
| MKNK1 | ENSG00000079277 | 0.00 | 0.00 | 0 | 0 |
| TLR5 | ENSG00000187554 | 0.00 | 0.00 | 0 | 0 |
| TGM3 | ENSG00000125780 | 0.00 | 0.00 | 0 | 0 |
| RANBP9 | ENSG00000010017 | 0.41 | 0.30 | 2 | 2 |
| CNTN1 | ENSG00000018236 | 0.00 | 0.00 | 0 | 0 |
| SLC30A8 | ENSG00000164756 | 0.00 | 0.00 | 0 | 0 |
| NOTCH4 | ENSG00000204301 | 0.00 | 0.00 | 0 | 0 |
| GPR176 | ENSG00000166073 | 0.00 | 0.00 | 0 | 0 |
| TRHDE | ENSG00000072657 | 0.00 | 0.00 | 0 | 0 |
| RTN4R | ENSG00000040608 | 0.17 | 0.00 | 1 | 0 |
| CPE | ENSG00000109472 | 0.00 | 0.00 | 0 | 0 |
| ENPP6 | ENSG00000164303 | 0.00 | 0.00 | 0 | 0 |
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