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 |
| FABP5 | ENSG00000164687 | 0.36 | 0.00 | 2 | 0 |
| SLC13A4 | ENSG00000164707 | 0.00 | 0.00 | 0 | 0 |
| HNF4G | ENSG00000164749 | 0.00 | 0.00 | 0 | 0 |
| KCNV1 | ENSG00000164794 | 0.00 | 0.00 | 0 | 0 |
| DEFA5 | ENSG00000164816 | 0.00 | 0.00 | 0 | 0 |
| DEFA4 | ENSG00000164821 | 0.00 | 0.00 | 0 | 0 |
| DEFA6 | ENSG00000164822 | 0.00 | 0.00 | 0 | 0 |
| DEFB1 | ENSG00000164825 | 0.00 | 0.00 | 0 | 0 |
| GPER1 | ENSG00000164850 | 0.00 | 0.40 | 0 | 1 |
| SPAG11B | ENSG00000164871 | 0.00 | 0.00 | 0 | 0 |
| CDK5 | ENSG00000164885 | 0.10 | 0.19 | 1 | 1 |
| SLC4A2 | ENSG00000164889 | 0.10 | 0.19 | 1 | 1 |
| SLC7A13 | ENSG00000164893 | 0.00 | 0.00 | 0 | 0 |
| FZD6 | ENSG00000164930 | 0.14 | 0.00 | 1 | 0 |
| CTHRC1 | ENSG00000164932 | 0.14 | 0.00 | 1 | 0 |
| KIAA1161 | ENSG00000164976 | 0.18 | 0.00 | 1 | 0 |
| PRKACG | ENSG00000165059 | 0.00 | 0.00 | 0 | 0 |
| PRSS37 | ENSG00000165076 | 0.00 | 0.00 | 0 | 0 |
| FBP1 | ENSG00000165140 | 0.00 | 0.00 | 0 | 0 |
| CYBB | ENSG00000165168 | 0.00 | 0.00 | 0 | 0 |
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