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 |
| HTR2C | ENSG00000147246 | 0.00 | 0.00 | 0 | 0 |
| ATG4C | ENSG00000125703 | 0.00 | 0.00 | 0 | 0 |
| SLC22A16 | ENSG00000004809 | 0.00 | 0.00 | 0 | 0 |
| GFPT1 | ENSG00000198380 | 0.00 | 0.00 | 0 | 0 |
| CD40 | ENSG00000101017 | 0.00 | 0.00 | 0 | 0 |
| CSAD | ENSG00000139631 | 0.00 | 0.00 | 0 | 0 |
| MAP4K3 | ENSG00000011566 | 0.18 | 0.00 | 1 | 0 |
| GPR156 | ENSG00000175697 | 0.00 | 0.00 | 0 | 0 |
| SLC8B1 | ENSG00000089060 | 0.00 | 0.00 | 0 | 0 |
| AQP1 | ENSG00000240583 | 0.00 | 0.00 | 0 | 0 |
| PRKD3 | ENSG00000115825 | 0.13 | 0.00 | 1 | 0 |
| CHRNE | ENSG00000108556 | 0.00 | 0.12 | 0 | 1 |
| NLN | ENSG00000123213 | 0.00 | 0.00 | 0 | 0 |
| TNKS2 | ENSG00000107854 | 0.00 | 0.45 | 0 | 2 |
| UCHL5 | ENSG00000116750 | 0.10 | 0.00 | 1 | 0 |
| HIATL1 | ENSG00000148110 | 0.00 | 0.11 | 0 | 1 |
| MLH1 | ENSG00000076242 | 0.00 | 0.18 | 0 | 1 |
| SIRT6 | ENSG00000077463 | 0.00 | 0.74 | 0 | 1 |
| PRKAR2A | ENSG00000114302 | 0.00 | 0.94 | 0 | 5 |
| GLB1 | ENSG00000170266 | 0.00 | 0.18 | 0 | 1 |
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