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 |
| BPHL | ENSG00000137274 | 0.61 | 0.38 | 3 | 2 |
| ATP11C | ENSG00000101974 | 0.13 | 0.00 | 1 | 0 |
| SLC25A39 | ENSG00000013306 | 0.00 | 0.17 | 0 | 1 |
| CYP1B1 | ENSG00000138061 | 0.00 | 0.00 | 0 | 0 |
| SLC22A4 | ENSG00000197208 | 0.28 | 0.00 | 1 | 0 |
| LIMK1 | ENSG00000106683 | 0.12 | 0.00 | 1 | 0 |
| GRN | ENSG00000030582 | 0.00 | 0.33 | 0 | 2 |
| BRDT | ENSG00000137948 | 0.00 | 0.00 | 0 | 0 |
| ALDH5A1 | ENSG00000112294 | 0.00 | 0.00 | 0 | 0 |
| VDR | ENSG00000111424 | 0.00 | 0.00 | 0 | 0 |
| TBXAS1 | ENSG00000059377 | 0.00 | 0.00 | 0 | 0 |
| ACHE | ENSG00000087085 | 0.00 | 0.00 | 0 | 0 |
| ORM2 | ENSG00000228278 | 0.00 | 0.00 | 0 | 0 |
| UGT1A6 | ENSG00000167165 | 0.00 | 0.00 | 0 | 0 |
| BMX | ENSG00000102010 | 0.00 | 0.00 | 0 | 0 |
| UHMK1 | ENSG00000152332 | 0.37 | 0.00 | 2 | 0 |
| PDE5A | ENSG00000138735 | 0.00 | 0.00 | 0 | 0 |
| CAMK1D | ENSG00000183049 | 0.18 | 0.00 | 1 | 0 |
| SFRP1 | ENSG00000104332 | 0.00 | 0.00 | 0 | 0 |
| BSG | ENSG00000172270 | 0.00 | 0.47 | 0 | 3 |
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