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 |
| GLRA4 | ENSG00000188828 | 0.00 | 0.00 | 0 | 0 |
| ASTL | ENSG00000188886 | 0.00 | 0.00 | 0 | 0 |
| NYX | ENSG00000188937 | 0.00 | 0.00 | 0 | 0 |
| SLC15A5 | ENSG00000188991 | 0.00 | 0.00 | 0 | 0 |
| SBSN | ENSG00000189001 | 0.00 | 0.00 | 0 | 0 |
| KIR2DL4 | ENSG00000189013 | 0.00 | 0.00 | 0 | 0 |
| DUSP21 | ENSG00000189037 | 0.00 | 0.00 | 0 | 0 |
| NDUFA4 | ENSG00000189043 | 0.00 | 0.00 | 0 | 0 |
| APOD | ENSG00000189058 | 0.00 | 0.00 | 0 | 0 |
| H1F0 | ENSG00000189060 | 0.00 | 0.00 | 0 | 0 |
| PRSS48 | ENSG00000189099 | 0.00 | 0.00 | 0 | 0 |
| S100A13 | ENSG00000189171 | 0.20 | 0.00 | 1 | 0 |
| OR14I1 | ENSG00000189181 | 0.00 | 0.00 | 0 | 0 |
| CXCL17 | ENSG00000189377 | 0.00 | 0.00 | 0 | 0 |
| HMGB1 | ENSG00000189403 | 0.16 | 0.18 | 1 | 1 |
| MMP23B | ENSG00000189409 | 0.00 | 0.00 | 0 | 0 |
| NCR1 | ENSG00000189430 | 0.00 | 0.00 | 0 | 0 |
| OR2L13 | ENSG00000196071 | 0.00 | 0.00 | 0 | 0 |
| OR5K4 | ENSG00000196098 | 0.00 | 0.00 | 0 | 0 |
| OR6M1 | ENSG00000196099 | 0.00 | 0.00 | 0 | 0 |
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