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 |
| HLCS | ENSG00000159267 | 0.13 | 0.00 | 1 | 0 |
| SLC39A5 | ENSG00000139540 | 0.00 | 0.00 | 0 | 0 |
| ULK4 | ENSG00000168038 | 0.00 | 0.18 | 0 | 1 |
| PLD2 | ENSG00000129219 | 0.00 | 0.12 | 0 | 1 |
| NELL2 | ENSG00000184613 | 0.00 | 0.00 | 0 | 0 |
| GPR61 | ENSG00000156097 | 0.00 | 0.00 | 0 | 0 |
| GSK3A | ENSG00000105723 | 0.00 | 0.57 | 0 | 3 |
| COL25A1 | ENSG00000188517 | 0.00 | 0.00 | 0 | 0 |
| RPS6KB2 | ENSG00000175634 | 0.50 | 0.00 | 2 | 0 |
| KCNJ2 | ENSG00000123700 | 0.20 | 0.00 | 1 | 0 |
| CES2 | ENSG00000172831 | 0.15 | 0.14 | 1 | 1 |
| ZRANB1 | ENSG00000019995 | 0.00 | 0.42 | 0 | 3 |
| KIAA0195 | ENSG00000177728 | 1.33 | 0.00 | 6 | 0 |
| GABRB3 | ENSG00000166206 | 0.00 | 0.12 | 0 | 1 |
| SLC38A7 | ENSG00000103042 | 0.12 | 0.16 | 1 | 1 |
| HPN | ENSG00000105707 | 0.00 | 0.00 | 0 | 0 |
| DSTYK | ENSG00000133059 | 0.12 | 0.00 | 1 | 0 |
| SETMAR | ENSG00000170364 | 0.00 | 0.52 | 0 | 3 |
| CP | ENSG00000047457 | 0.00 | 0.00 | 0 | 0 |
| TDP2 | ENSG00000111802 | 0.00 | 0.00 | 0 | 0 |
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