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 |
| SLC7A2 | ENSG00000003989 | 0.00 | 0.12 | 0 | 1 |
| PAPLN | ENSG00000100767 | 0.00 | 0.22 | 0 | 2 |
| PPARA | ENSG00000186951 | 0.00 | 0.51 | 0 | 3 |
| PPOX | ENSG00000143224 | 0.57 | 0.00 | 3 | 0 |
| CDK18 | ENSG00000117266 | 0.00 | 0.00 | 0 | 0 |
| PRKAA2 | ENSG00000162409 | 0.00 | 0.00 | 0 | 0 |
| PDE7B | ENSG00000171408 | 0.00 | 0.11 | 0 | 1 |
| PTPRG | ENSG00000144724 | 0.00 | 0.40 | 0 | 3 |
| CDK8 | ENSG00000132964 | 0.00 | 0.18 | 0 | 1 |
| SLC5A11 | ENSG00000158865 | 0.00 | 0.00 | 0 | 0 |
| RHBDL1 | ENSG00000103269 | 0.00 | 0.35 | 0 | 2 |
| SND1 | ENSG00000197157 | 0.11 | 0.29 | 1 | 2 |
| DPP3 | ENSG00000254986 | 0.29 | 0.00 | 1 | 0 |
| ADH6 | ENSG00000172955 | 0.00 | 0.00 | 0 | 0 |
| CHRNB1 | ENSG00000170175 | 0.00 | 0.15 | 0 | 1 |
| ADAMDEC1 | ENSG00000134028 | 0.00 | 0.00 | 0 | 0 |
| GPR161 | ENSG00000143147 | 0.00 | 0.00 | 0 | 0 |
| MAP4K4 | ENSG00000071054 | 0.00 | 0.00 | 0 | 0 |
| NID1 | ENSG00000116962 | 0.00 | 0.00 | 0 | 0 |
| VWF | ENSG00000110799 | 0.00 | 0.00 | 0 | 0 |
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