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 |
| SYK | ENSG00000165025 | 0.00 | 0.00 | 0 | 0 |
| MGAM | ENSG00000257335 | 0.00 | 0.00 | 0 | 0 |
| VCP | ENSG00000165280 | 0.14 | 0.00 | 1 | 0 |
| ACTN2 | ENSG00000077522 | 0.16 | 0.00 | 1 | 0 |
| EGLN1 | ENSG00000135766 | 0.49 | 0.23 | 3 | 1 |
| PTPRD | ENSG00000153707 | 0.00 | 0.76 | 0 | 4 |
| LAMA2 | ENSG00000196569 | 0.00 | 0.13 | 0 | 1 |
| VEGFC | ENSG00000150630 | 0.00 | 0.30 | 0 | 2 |
| KLK3 | ENSG00000142515 | 0.23 | 0.00 | 1 | 0 |
| TNXB | ENSG00000168477 | 0.00 | 0.00 | 0 | 0 |
| GPR146 | ENSG00000164849 | 0.15 | 0.40 | 1 | 1 |
| MAP3K2 | ENSG00000169967 | 0.00 | 0.00 | 0 | 0 |
| MTR | ENSG00000116984 | 0.53 | 0.25 | 3 | 1 |
| COL22A1 | ENSG00000169436 | 0.50 | 0.00 | 1 | 0 |
| ATP2A2 | ENSG00000174437 | 0.00 | 0.00 | 0 | 0 |
| KLK2 | ENSG00000167751 | 0.23 | 0.00 | 1 | 0 |
| SERPIND1 | ENSG00000099937 | 0.00 | 0.00 | 0 | 0 |
| ERMP1 | ENSG00000099219 | 0.42 | 0.31 | 2 | 2 |
| MTMR2 | ENSG00000087053 | 0.00 | 0.19 | 0 | 1 |
| SCD5 | ENSG00000145284 | 0.00 | 0.00 | 0 | 0 |
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