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 |
| AXIN2 | ENSG00000168646 | 0.12 | 0.00 | 1 | 0 |
| KCNK5 | ENSG00000164626 | 0.00 | 0.00 | 0 | 0 |
| SLC7A1 | ENSG00000139514 | 0.00 | 0.00 | 0 | 0 |
| CD1C | ENSG00000158481 | 0.00 | 0.00 | 0 | 0 |
| MMEL1 | ENSG00000142606 | 0.00 | 0.11 | 0 | 1 |
| CHRNB4 | ENSG00000117971 | 0.13 | 0.00 | 1 | 0 |
| ABAT | ENSG00000183044 | 0.28 | 0.00 | 1 | 0 |
| FNTA | ENSG00000168522 | 1.02 | 0.00 | 1 | 0 |
| SERPINH1 | ENSG00000149257 | 0.43 | 0.00 | 1 | 0 |
| COL5A1 | ENSG00000130635 | 0.00 | 0.25 | 0 | 1 |
| NFKB2 | ENSG00000077150 | 0.00 | 0.59 | 0 | 3 |
| POLA1 | ENSG00000101868 | 0.20 | 0.00 | 1 | 0 |
| CACNG8 | ENSG00000142408 | 0.00 | 0.00 | 0 | 0 |
| ITGA4 | ENSG00000115232 | 0.00 | 0.00 | 0 | 0 |
| PKM | ENSG00000067225 | 0.00 | 0.00 | 0 | 0 |
| WNT2 | ENSG00000105989 | 0.00 | 0.00 | 0 | 0 |
| CHRNA3 | ENSG00000080644 | 0.00 | 0.00 | 0 | 0 |
| ITGB5 | ENSG00000082781 | 0.00 | 0.00 | 0 | 0 |
| CA14 | ENSG00000118298 | 0.54 | 0.00 | 3 | 0 |
| ASH2L | ENSG00000129691 | 0.25 | 0.00 | 1 | 0 |
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