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 |
| STAT1 | ENSG00000115415 | 0.12 | 0.00 | 1 | 0 |
| SLCO2B1 | ENSG00000137491 | 0.00 | 0.00 | 0 | 0 |
| NPEPPS | ENSG00000141279 | 0.00 | 0.19 | 0 | 1 |
| PHF21A | ENSG00000135365 | 0.31 | 0.00 | 2 | 0 |
| CA10 | ENSG00000154975 | 0.00 | 0.00 | 0 | 0 |
| AGXT2 | ENSG00000113492 | 0.00 | 0.00 | 0 | 0 |
| CYP39A1 | ENSG00000146233 | 0.00 | 0.00 | 0 | 0 |
| PRKD1 | ENSG00000184304 | 0.00 | 0.00 | 0 | 0 |
| GUCY2C | ENSG00000070019 | 0.00 | 0.00 | 0 | 0 |
| AEBP1 | ENSG00000106624 | 0.00 | 0.00 | 0 | 0 |
| SLC9A9 | ENSG00000181804 | 0.00 | 0.00 | 0 | 0 |
| CTSS | ENSG00000163131 | 0.25 | 0.00 | 1 | 0 |
| ANTXR1 | ENSG00000169604 | 0.00 | 0.00 | 0 | 0 |
| SLC26A9 | ENSG00000174502 | 0.00 | 0.00 | 0 | 0 |
| SLC4A7 | ENSG00000033867 | 0.00 | 0.00 | 0 | 0 |
| AOC1 | ENSG00000002726 | 0.00 | 0.00 | 0 | 0 |
| TDRD10 | ENSG00000163239 | 0.00 | 0.00 | 0 | 0 |
| GBE1 | ENSG00000114480 | 0.00 | 0.11 | 0 | 1 |
| REG1A | ENSG00000115386 | 0.00 | 0.00 | 0 | 0 |
| MARK4 | ENSG00000007047 | 0.16 | 0.46 | 1 | 2 |
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