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 |
| CTNNB1 | ENSG00000168036 | 0.00 | 0.00 | 0 | 0 |
| IGF1R | ENSG00000140443 | 1.76 | 0.00 | 7 | 0 |
| EIF4A1 | ENSG00000161960 | 0.00 | 0.16 | 0 | 1 |
| EPHA2 | ENSG00000142627 | 0.00 | 0.53 | 0 | 3 |
| RIOK1 | ENSG00000124784 | 0.40 | 0.36 | 2 | 2 |
| MECOM | ENSG00000085276 | 0.00 | 0.00 | 0 | 0 |
| TFRC | ENSG00000072274 | 0.55 | 0.14 | 2 | 1 |
| TLN1 | ENSG00000137076 | 1.07 | 0.13 | 4 | 1 |
| PDE4D | ENSG00000113448 | 0.00 | 2.51 | 0 | 9 |
| AKT1 | ENSG00000142208 | 0.58 | 0.45 | 2 | 2 |
| PNMT | ENSG00000141744 | 2.81 | 0.00 | 4 | 0 |
| USP5 | ENSG00000111667 | 0.60 | 0.00 | 1 | 0 |
| CPM | ENSG00000135678 | 1.49 | 0.00 | 4 | 0 |
| ATAD2 | ENSG00000156802 | 1.54 | 0.00 | 5 | 0 |
| CDC25A | ENSG00000164045 | 0.00 | 0.32 | 0 | 2 |
| PTPRN2 | ENSG00000155093 | 0.00 | 0.11 | 0 | 1 |
| TNFSF10 | ENSG00000121858 | 0.94 | 0.00 | 2 | 0 |
| GGPS1 | ENSG00000152904 | 1.11 | 0.24 | 4 | 1 |
| ATP6V1B2 | ENSG00000147416 | 0.00 | 0.79 | 0 | 5 |
| TRIO | ENSG00000038382 | 0.00 | 0.00 | 0 | 0 |
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