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 |
| VEGFB | ENSG00000173511 | 0.11 | 0.00 | 1 | 0 |
| PEAK1 | ENSG00000173517 | 0.13 | 0.00 | 1 | 0 |
| TNFRSF10D | ENSG00000173530 | 0.00 | 0.76 | 0 | 5 |
| MST1 | ENSG00000173531 | 0.00 | 0.66 | 0 | 4 |
| TNFRSF10C | ENSG00000173535 | 0.00 | 1.28 | 0 | 8 |
| ADGRF3 | ENSG00000173567 | 0.00 | 0.00 | 0 | 0 |
| XCR1 | ENSG00000173578 | 0.00 | 0.00 | 0 | 0 |
| CCR9 | ENSG00000173585 | 0.00 | 0.00 | 0 | 0 |
| UGT2A1 | ENSG00000173610 | 0.00 | 0.00 | 0 | 0 |
| GPRC6A | ENSG00000173612 | 0.00 | 0.00 | 0 | 0 |
| SLC19A1 | ENSG00000173638 | 0.10 | 0.18 | 1 | 1 |
| RCE1 | ENSG00000173653 | 0.36 | 0.00 | 2 | 0 |
| OR1L1 | ENSG00000173679 | 0.00 | 0.00 | 0 | 0 |
| ADGRG2 | ENSG00000173698 | 0.15 | 0.00 | 1 | 0 |
| MUC13 | ENSG00000173702 | 0.00 | 0.00 | 0 | 0 |
| CD7 | ENSG00000173762 | 0.00 | 0.00 | 0 | 0 |
| KCNH6 | ENSG00000173826 | 0.00 | 0.00 | 0 | 0 |
| PLK3 | ENSG00000173846 | 0.00 | 0.00 | 0 | 0 |
| CBX2 | ENSG00000173894 | 0.86 | 0.00 | 3 | 0 |
| SLCO4C1 | ENSG00000173930 | 0.00 | 0.00 | 0 | 0 |
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