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 |
| ATP1B1 | ENSG00000143153 | 0.00 | 0.00 | 0 | 0 |
| CREG1 | ENSG00000143162 | 0.22 | 0.00 | 1 | 0 |
| GPA33 | ENSG00000143167 | 0.00 | 0.00 | 0 | 0 |
| XCL1 | ENSG00000143184 | 0.00 | 0.00 | 0 | 0 |
| XCL2 | ENSG00000143185 | 0.00 | 0.00 | 0 | 0 |
| MGST3 | ENSG00000143198 | 0.21 | 0.00 | 1 | 0 |
| NR1I3 | ENSG00000143257 | 0.00 | 0.00 | 0 | 0 |
| FCRL5 | ENSG00000143297 | 0.00 | 0.00 | 0 | 0 |
| CRABP2 | ENSG00000143320 | 0.00 | 0.00 | 0 | 0 |
| HDGF | ENSG00000143321 | 1.06 | 0.00 | 5 | 0 |
| ECM1 | ENSG00000143369 | 0.45 | 0.00 | 1 | 0 |
| ADAMTSL4 | ENSG00000143382 | 0.45 | 0.00 | 1 | 0 |
| CTSK | ENSG00000143387 | 0.47 | 0.00 | 1 | 0 |
| DYRK3 | ENSG00000143479 | 0.00 | 0.00 | 0 | 0 |
| TAF1A | ENSG00000143498 | 0.00 | 0.22 | 0 | 1 |
| S100A8 | ENSG00000143546 | 0.00 | 0.00 | 0 | 0 |
| SLC27A3 | ENSG00000143554 | 1.05 | 0.00 | 4 | 0 |
| S100A7 | ENSG00000143556 | 0.00 | 0.00 | 0 | 0 |
| SLC39A1 | ENSG00000143570 | 1.94 | 0.00 | 7 | 0 |
| AQP10 | ENSG00000143595 | 0.00 | 0.00 | 0 | 0 |
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