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 |
| TRPV3 | ENSG00000167723 | 0.00 | 0.00 | 0 | 0 |
| GPR162 | ENSG00000250510 | 0.60 | 0.00 | 1 | 0 |
| NLRP3 | ENSG00000162711 | 0.00 | 0.00 | 0 | 0 |
| PTPN12 | ENSG00000127947 | 0.00 | 0.00 | 0 | 0 |
| SLC1A2 | ENSG00000110436 | 0.00 | 0.00 | 0 | 0 |
| ACVR2A | ENSG00000121989 | 0.00 | 0.17 | 0 | 1 |
| KLHL35 | ENSG00000149243 | 0.49 | 0.00 | 1 | 0 |
| KCNAB2 | ENSG00000069424 | 0.00 | 0.59 | 0 | 3 |
| LINGO1 | ENSG00000169783 | 0.00 | 0.00 | 0 | 0 |
| PTGR2 | ENSG00000140043 | 0.00 | 0.22 | 0 | 2 |
| CACNA1G | ENSG00000006283 | 0.00 | 0.00 | 0 | 0 |
| SLC25A27 | ENSG00000153291 | 0.00 | 0.00 | 0 | 0 |
| AGPAT2 | ENSG00000169692 | 0.00 | 0.39 | 0 | 2 |
| CPA3 | ENSG00000163751 | 0.00 | 0.00 | 0 | 0 |
| GC | ENSG00000145321 | 0.00 | 0.00 | 0 | 0 |
| KCNQ3 | ENSG00000184156 | 0.00 | 0.00 | 0 | 0 |
| CDC42BPG | ENSG00000171219 | 0.00 | 0.00 | 0 | 0 |
| SLC7A7 | ENSG00000155465 | 0.00 | 0.00 | 0 | 0 |
| PRKACA | ENSG00000072062 | 0.00 | 0.00 | 0 | 0 |
| WNT11 | ENSG00000085741 | 0.00 | 0.00 | 0 | 0 |
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