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 |
| EHMT1 | ENSG00000181090 | 0.00 | 0.33 | 0 | 2 |
| PHF14 | ENSG00000106443 | 0.00 | 0.00 | 0 | 0 |
| NPC1 | ENSG00000141458 | 0.13 | 0.00 | 1 | 0 |
| SLC20A2 | ENSG00000168575 | 0.83 | 0.00 | 3 | 0 |
| SLC41A2 | ENSG00000136052 | 0.00 | 0.00 | 0 | 0 |
| GAA | ENSG00000171298 | 1.25 | 0.00 | 5 | 0 |
| MECR | ENSG00000116353 | 0.00 | 0.59 | 0 | 3 |
| DLD | ENSG00000091140 | 0.00 | 0.00 | 0 | 0 |
| IGSF8 | ENSG00000162729 | 0.38 | 0.00 | 2 | 0 |
| RTN4 | ENSG00000115310 | 0.00 | 0.00 | 0 | 0 |
| SETD4 | ENSG00000185917 | 0.00 | 0.00 | 0 | 0 |
| SLC30A9 | ENSG00000014824 | 0.00 | 0.00 | 0 | 0 |
| STIM2 | ENSG00000109689 | 0.00 | 0.00 | 0 | 0 |
| CLK1 | ENSG00000013441 | 0.14 | 0.00 | 1 | 0 |
| RGS12 | ENSG00000159788 | 0.00 | 0.00 | 0 | 0 |
| PDE4A | ENSG00000065989 | 0.00 | 0.00 | 0 | 0 |
| IDS | ENSG00000010404 | 0.15 | 0.00 | 1 | 0 |
| SCYL3 | ENSG00000000457 | 0.30 | 0.00 | 2 | 0 |
| F13A1 | ENSG00000124491 | 0.00 | 0.00 | 0 | 0 |
| PMS2 | ENSG00000122512 | 0.59 | 0.41 | 4 | 1 |
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