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 |
| KNG1 | ENSG00000113889 | 0.00 | 0.00 | 0 | 0 |
| GPR158 | ENSG00000151025 | 0.00 | 0.00 | 0 | 0 |
| ME1 | ENSG00000065833 | 0.00 | 0.00 | 0 | 0 |
| SULF1 | ENSG00000137573 | 0.00 | 0.00 | 0 | 0 |
| CLCN6 | ENSG00000011021 | 0.00 | 2.01 | 0 | 6 |
| SCUBE2 | ENSG00000175356 | 0.00 | 0.00 | 0 | 0 |
| HGF | ENSG00000019991 | 0.00 | 0.00 | 0 | 0 |
| IKBKE | ENSG00000263528 | 0.12 | 0.00 | 1 | 0 |
| KMO | ENSG00000117009 | 0.26 | 0.00 | 1 | 0 |
| SUV420H2 | ENSG00000133247 | 0.37 | 0.29 | 2 | 2 |
| SEPP1 | ENSG00000250722 | 0.19 | 0.00 | 1 | 0 |
| CLDN18 | ENSG00000066405 | 0.00 | 0.00 | 0 | 0 |
| TENM1 | ENSG00000009694 | 0.00 | 0.00 | 0 | 0 |
| ADAM19 | ENSG00000135074 | 0.00 | 0.00 | 0 | 0 |
| WHSC1 | ENSG00000109685 | 0.53 | 0.00 | 2 | 0 |
| RBM10 | ENSG00000182872 | 0.00 | 0.00 | 0 | 0 |
| SORD | ENSG00000140263 | 0.00 | 0.15 | 0 | 1 |
| SLC25A3 | ENSG00000075415 | 0.00 | 0.17 | 0 | 1 |
| KCNG3 | ENSG00000171126 | 0.00 | 0.00 | 0 | 0 |
| MMP14 | ENSG00000157227 | 0.00 | 0.00 | 0 | 0 |
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