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 |
| C6 | ENSG00000039537 | 0.00 | 0.00 | 0 | 0 |
| PSMA4 | ENSG00000041357 | 0.12 | 0.00 | 1 | 0 |
| AIFM2 | ENSG00000042286 | 0.00 | 0.00 | 0 | 0 |
| JADE2 | ENSG00000043143 | 0.28 | 0.00 | 1 | 0 |
| ADRB1 | ENSG00000043591 | 0.00 | 0.00 | 0 | 0 |
| GUCA2B | ENSG00000044012 | 0.00 | 0.00 | 0 | 0 |
| HSPA5 | ENSG00000044574 | 0.00 | 0.00 | 0 | 0 |
| TNFRSF17 | ENSG00000048462 | 0.00 | 0.00 | 0 | 0 |
| UTS2 | ENSG00000049247 | 0.00 | 0.00 | 0 | 0 |
| TNFRSF9 | ENSG00000049249 | 0.00 | 0.11 | 0 | 1 |
| RAD51 | ENSG00000051180 | 0.00 | 0.28 | 0 | 2 |
| PRSS8 | ENSG00000052344 | 0.10 | 0.00 | 1 | 0 |
| AKR7A2 | ENSG00000053371 | 0.00 | 1.13 | 0 | 6 |
| LY75 | ENSG00000054219 | 0.00 | 0.00 | 0 | 0 |
| PTPRN | ENSG00000054356 | 0.00 | 0.00 | 0 | 0 |
| CBLN4 | ENSG00000054803 | 0.00 | 0.00 | 0 | 0 |
| RELT | ENSG00000054967 | 0.59 | 0.00 | 1 | 0 |
| GALC | ENSG00000054983 | 0.00 | 0.42 | 0 | 2 |
| MCOLN3 | ENSG00000055732 | 0.00 | 0.00 | 0 | 0 |
| ITIH4 | ENSG00000055955 | 0.00 | 0.55 | 0 | 3 |
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