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 |
| TAC3 | ENSG00000166863 | 0.00 | 0.00 | 0 | 0 |
| OR4D6 | ENSG00000166884 | 0.00 | 0.00 | 0 | 0 |
| XRCC6BP1 | ENSG00000166896 | 0.39 | 0.00 | 1 | 0 |
| SCG5 | ENSG00000166922 | 0.00 | 0.00 | 0 | 0 |
| GREM1 | ENSG00000166923 | 0.00 | 0.00 | 0 | 0 |
| EPB42 | ENSG00000166947 | 0.00 | 0.00 | 0 | 0 |
| TGM6 | ENSG00000166948 | 0.00 | 0.00 | 0 | 0 |
| MARS | ENSG00000166986 | 0.00 | 0.00 | 0 | 0 |
| PDIA3 | ENSG00000167004 | 0.00 | 0.61 | 0 | 3 |
| DUSP18 | ENSG00000167065 | 0.23 | 0.00 | 1 | 0 |
| BPIFB6 | ENSG00000167104 | 0.00 | 0.00 | 0 | 0 |
| ENDOG | ENSG00000167136 | 0.00 | 0.00 | 0 | 0 |
| ISLR2 | ENSG00000167178 | 0.00 | 0.00 | 0 | 0 |
| IGF2 | ENSG00000167244 | 0.39 | 0.00 | 2 | 0 |
| CD3D | ENSG00000167286 | 0.00 | 0.23 | 0 | 1 |
| OR51I1 | ENSG00000167359 | 0.00 | 0.00 | 0 | 0 |
| OR51Q1 | ENSG00000167360 | 0.00 | 0.00 | 0 | 0 |
| VKORC1 | ENSG00000167397 | 0.11 | 0.00 | 1 | 0 |
| GPX4 | ENSG00000167468 | 0.00 | 1.45 | 0 | 5 |
| MVD | ENSG00000167508 | 0.00 | 0.81 | 0 | 5 |
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