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 |
| PAK6 | ENSG00000137843 | 0.00 | 0.29 | 0 | 2 |
| DUOX1 | ENSG00000137857 | 0.00 | 0.00 | 0 | 0 |
| SLC28A2 | ENSG00000137860 | 0.00 | 0.00 | 0 | 0 |
| BCL2L10 | ENSG00000137875 | 0.00 | 0.00 | 0 | 0 |
| CLCA2 | ENSG00000137975 | 0.00 | 0.00 | 0 | 0 |
| CGREF1 | ENSG00000138028 | 0.00 | 0.00 | 0 | 0 |
| KHK | ENSG00000138030 | 0.17 | 0.00 | 1 | 0 |
| LHCGR | ENSG00000138039 | 0.00 | 0.00 | 0 | 0 |
| ABCG5 | ENSG00000138075 | 0.00 | 0.00 | 0 | 0 |
| PREPL | ENSG00000138078 | 0.00 | 0.00 | 0 | 0 |
| EMILIN1 | ENSG00000138080 | 0.00 | 0.00 | 0 | 0 |
| ATRAID | ENSG00000138085 | 0.17 | 0.00 | 1 | 0 |
| DUSP5 | ENSG00000138166 | 0.00 | 0.11 | 0 | 1 |
| RBP4 | ENSG00000138207 | 0.00 | 0.00 | 0 | 0 |
| GPR87 | ENSG00000138271 | 0.00 | 0.00 | 0 | 0 |
| PLA2G12B | ENSG00000138308 | 0.00 | 0.00 | 0 | 0 |
| AOX1 | ENSG00000138356 | 0.00 | 0.00 | 0 | 0 |
| MSTN | ENSG00000138379 | 0.00 | 0.00 | 0 | 0 |
| CDK15 | ENSG00000138395 | 0.00 | 0.00 | 0 | 0 |
| CHRNA1 | ENSG00000138435 | 0.00 | 0.00 | 0 | 0 |
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