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 |
| HHIP | ENSG00000164161 | 0.00 | 0.00 | 0 | 0 |
| COCH | ENSG00000100473 | 0.00 | 0.00 | 0 | 0 |
| LGALS8 | ENSG00000116977 | 0.54 | 0.24 | 3 | 1 |
| FXR2 | ENSG00000129245 | 0.00 | 0.65 | 0 | 4 |
| KMT2E | ENSG00000005483 | 0.00 | 0.00 | 0 | 0 |
| MMP2 | ENSG00000087245 | 0.00 | 0.00 | 0 | 0 |
| SLC7A9 | ENSG00000021488 | 0.00 | 0.00 | 0 | 0 |
| GART | ENSG00000159131 | 0.00 | 0.00 | 0 | 0 |
| KCNQ5 | ENSG00000185760 | 0.00 | 0.00 | 0 | 0 |
| CATSPER1 | ENSG00000175294 | 0.00 | 0.00 | 0 | 0 |
| ITGA9 | ENSG00000144668 | 0.00 | 0.00 | 0 | 0 |
| AHSG | ENSG00000145192 | 0.00 | 0.00 | 0 | 0 |
| THRA | ENSG00000126351 | 0.00 | 0.00 | 0 | 0 |
| AGRN | ENSG00000188157 | 0.00 | 0.66 | 0 | 3 |
| RECK | ENSG00000122707 | 0.00 | 0.00 | 0 | 0 |
| ITIH3 | ENSG00000162267 | 0.00 | 0.34 | 0 | 2 |
| SLC5A6 | ENSG00000138074 | 0.17 | 0.00 | 1 | 0 |
| PRKG1 | ENSG00000185532 | 0.00 | 0.00 | 0 | 0 |
| TP53BP1 | ENSG00000067369 | 0.00 | 0.61 | 0 | 3 |
| TAOK1 | ENSG00000160551 | 0.28 | 0.00 | 1 | 0 |
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