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 |
| PPARG | ENSG00000132170 | 0.76 | 0.00 | 1 | 0 |
| HRAS | ENSG00000174775 | 0.00 | 1.37 | 0 | 7 |
| CD79B | ENSG00000007312 | 0.00 | 0.00 | 0 | 0 |
| TYRP1 | ENSG00000107165 | 0.00 | 0.00 | 0 | 0 |
| FGFR1 | ENSG00000077782 | 0.41 | 0.00 | 2 | 0 |
| KMT2C | ENSG00000055609 | 0.64 | 0.41 | 2 | 3 |
| ANO1 | ENSG00000131620 | 4.28 | 0.00 | 3 | 0 |
| TERT | ENSG00000164362 | 0.73 | 0.00 | 3 | 0 |
| CCND2 | ENSG00000118971 | 0.74 | 0.00 | 2 | 0 |
| KAT6B | ENSG00000156650 | 0.65 | 0.00 | 1 | 0 |
| ERBB3 | ENSG00000065361 | 0.22 | 0.00 | 1 | 0 |
| CDH1 | ENSG00000039068 | 0.16 | 0.35 | 1 | 1 |
| PDGFRA | ENSG00000134853 | 0.25 | 0.00 | 1 | 0 |
| PKMYT1 | ENSG00000127564 | 0.00 | 0.00 | 0 | 0 |
| SQLE | ENSG00000104549 | 1.48 | 0.00 | 5 | 0 |
| MCL1 | ENSG00000143384 | 4.28 | 0.00 | 11 | 0 |
| POLE | ENSG00000177084 | 0.00 | 0.54 | 0 | 3 |
| SLC16A3 | ENSG00000141526 | 0.00 | 0.10 | 0 | 1 |
| CCND3 | ENSG00000112576 | 0.57 | 0.00 | 3 | 0 |
| ATR | ENSG00000175054 | 0.00 | 0.00 | 0 | 0 |
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