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 |
| NOD2 | ENSG00000167207 | 0.00 | 0.00 | 0 | 0 |
| NTN4 | ENSG00000074527 | 0.00 | 0.00 | 0 | 0 |
| PDIA6 | ENSG00000143870 | 0.16 | 0.17 | 1 | 1 |
| ALDH9A1 | ENSG00000143149 | 0.21 | 0.00 | 1 | 0 |
| SERPINB1 | ENSG00000021355 | 0.18 | 0.13 | 1 | 1 |
| KSR1 | ENSG00000141068 | 0.00 | 0.00 | 0 | 0 |
| SLC17A5 | ENSG00000119899 | 0.00 | 0.14 | 0 | 1 |
| MICAL3 | ENSG00000243156 | 0.00 | 0.00 | 0 | 0 |
| IL2RB | ENSG00000100385 | 0.00 | 0.00 | 0 | 0 |
| FXR1 | ENSG00000114416 | 0.38 | 0.00 | 2 | 0 |
| NRBP2 | ENSG00000185189 | 0.93 | 0.00 | 3 | 0 |
| EMID1 | ENSG00000186998 | 0.00 | 0.00 | 0 | 0 |
| IKBKG | ENSG00000269335 | 1.12 | 0.00 | 5 | 0 |
| GDF5 | ENSG00000125965 | 0.00 | 0.00 | 0 | 0 |
| SERPINI1 | ENSG00000163536 | 0.00 | 0.00 | 0 | 0 |
| G2E3 | ENSG00000092140 | 0.00 | 0.00 | 0 | 0 |
| COL15A1 | ENSG00000204291 | 0.00 | 0.00 | 0 | 0 |
| FOS | ENSG00000170345 | 0.00 | 0.10 | 0 | 1 |
| CYP2A6 | ENSG00000255974 | 0.00 | 0.00 | 0 | 0 |
| ATP8A2 | ENSG00000132932 | 0.00 | 0.00 | 0 | 0 |
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