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 |
| TG | ENSG00000042832 | 0.37 | 0.00 | 2 | 0 |
| FGF9 | ENSG00000102678 | 0.00 | 0.22 | 0 | 1 |
| NOX4 | ENSG00000086991 | 0.00 | 0.00 | 0 | 0 |
| KL | ENSG00000133116 | 0.00 | 0.00 | 0 | 0 |
| RNASEH1 | ENSG00000171865 | 0.15 | 0.17 | 1 | 1 |
| KCNC3 | ENSG00000131398 | 0.23 | 0.32 | 1 | 1 |
| SPNS1 | ENSG00000169682 | 0.19 | 0.00 | 1 | 0 |
| CLCN2 | ENSG00000114859 | 0.39 | 0.10 | 2 | 1 |
| PMP2 | ENSG00000147588 | 0.00 | 0.00 | 0 | 0 |
| TMX2 | ENSG00000213593 | 0.00 | 0.11 | 0 | 1 |
| COL9A3 | ENSG00000092758 | 0.12 | 0.00 | 1 | 0 |
| KCNK2 | ENSG00000082482 | 0.00 | 0.16 | 0 | 1 |
| GRIK4 | ENSG00000149403 | 0.00 | 0.00 | 0 | 0 |
| GALK1 | ENSG00000108479 | 1.32 | 0.00 | 6 | 0 |
| MARK2 | ENSG00000072518 | 0.12 | 0.16 | 1 | 1 |
| HIPK1 | ENSG00000163349 | 0.00 | 0.49 | 0 | 3 |
| SERPINB7 | ENSG00000166396 | 0.00 | 0.00 | 0 | 0 |
| CEL | ENSG00000170835 | 0.00 | 0.24 | 0 | 1 |
| PIK3R5 | ENSG00000141506 | 0.00 | 0.15 | 0 | 1 |
| HP | ENSG00000257017 | 0.00 | 0.00 | 0 | 0 |
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