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 |
| SUPT16H | ENSG00000092201 | 0.29 | 0.00 | 1 | 0 |
| ASH1L | ENSG00000116539 | 1.00 | 0.00 | 3 | 0 |
| SAE1 | ENSG00000142230 | 0.00 | 0.63 | 0 | 3 |
| SP110 | ENSG00000135899 | 0.00 | 1.19 | 0 | 5 |
| CD8B | ENSG00000172116 | 0.00 | 0.00 | 0 | 0 |
| BCR | ENSG00000186716 | 0.00 | 0.00 | 0 | 0 |
| PRMT1 | ENSG00000126457 | 0.25 | 0.48 | 1 | 2 |
| BDH1 | ENSG00000161267 | 0.19 | 0.13 | 1 | 1 |
| TRRAP | ENSG00000196367 | 0.17 | 0.00 | 1 | 0 |
| BCAN | ENSG00000132692 | 0.60 | 0.00 | 2 | 0 |
| TK1 | ENSG00000167900 | 0.88 | 0.00 | 4 | 0 |
| PRAME | ENSG00000185686 | 0.00 | 0.00 | 0 | 0 |
| COL1A1 | ENSG00000108821 | 0.00 | 0.00 | 0 | 0 |
| NEIL3 | ENSG00000109674 | 0.00 | 0.28 | 0 | 2 |
| LONP1 | ENSG00000196365 | 0.00 | 0.00 | 0 | 0 |
| MAP2K1 | ENSG00000169032 | 0.00 | 0.00 | 0 | 0 |
| LMNA | ENSG00000160789 | 0.77 | 0.00 | 3 | 0 |
| PKLR | ENSG00000143627 | 0.19 | 0.00 | 1 | 0 |
| RET | ENSG00000165731 | 0.00 | 0.00 | 0 | 0 |
| BACE2 | ENSG00000182240 | 0.12 | 0.16 | 1 | 1 |
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