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 |
| PECR | ENSG00000115425 | 0.00 | 0.65 | 0 | 3 |
| CHD9 | ENSG00000177200 | 0.00 | 0.19 | 0 | 1 |
| TULP3 | ENSG00000078246 | 0.95 | 0.00 | 4 | 0 |
| MAST1 | ENSG00000105613 | 0.00 | 0.00 | 0 | 0 |
| PRKAG2 | ENSG00000106617 | 0.66 | 0.23 | 2 | 1 |
| TAF3 | ENSG00000165632 | 0.69 | 0.00 | 2 | 0 |
| YES1 | ENSG00000176105 | 0.18 | 0.12 | 1 | 1 |
| ZMPSTE24 | ENSG00000084073 | 0.28 | 0.00 | 2 | 0 |
| KCNMA1 | ENSG00000156113 | 0.00 | 0.00 | 0 | 0 |
| CACNA1E | ENSG00000198216 | 0.00 | 0.00 | 0 | 0 |
| CACNA1B | ENSG00000148408 | 0.00 | 0.00 | 0 | 0 |
| CDH13 | ENSG00000140945 | 0.00 | 0.11 | 0 | 1 |
| TMPRSS11E | ENSG00000087128 | 0.00 | 0.00 | 0 | 0 |
| NEK6 | ENSG00000119408 | 0.00 | 0.16 | 0 | 1 |
| CHD1 | ENSG00000153922 | 0.00 | 0.53 | 0 | 3 |
| SSTR5 | ENSG00000162009 | 0.00 | 0.00 | 0 | 0 |
| SLC39A14 | ENSG00000104635 | 0.00 | 1.14 | 0 | 7 |
| TNIK | ENSG00000154310 | 0.20 | 0.00 | 1 | 0 |
| CAMKK2 | ENSG00000110931 | 0.00 | 0.39 | 0 | 2 |
| NR6A1 | ENSG00000148200 | 0.00 | 0.16 | 0 | 1 |
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