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 |
| MME | ENSG00000196549 | 0.00 | 0.00 | 0 | 0 |
| NCOR2 | ENSG00000196498 | 0.00 | 0.12 | 0 | 1 |
| COL2A1 | ENSG00000139219 | 0.00 | 0.00 | 0 | 0 |
| DIDO1 | ENSG00000101191 | 0.43 | 0.00 | 3 | 0 |
| OLFML1 | ENSG00000183801 | 0.00 | 0.00 | 0 | 0 |
| PHIP | ENSG00000146247 | 0.00 | 0.14 | 0 | 1 |
| OPRL1 | ENSG00000125510 | 0.15 | 0.00 | 1 | 0 |
| ATP2C2 | ENSG00000064270 | 0.00 | 0.28 | 0 | 1 |
| TF | ENSG00000091513 | 0.00 | 0.00 | 0 | 0 |
| PDE6B | ENSG00000133256 | 0.42 | 0.00 | 1 | 0 |
| TLR4 | ENSG00000136869 | 0.00 | 0.00 | 0 | 0 |
| SMARCC1 | ENSG00000173473 | 0.00 | 0.91 | 0 | 5 |
| TAB2 | ENSG00000055208 | 0.00 | 0.48 | 0 | 3 |
| TGFBI | ENSG00000120708 | 0.00 | 0.00 | 0 | 0 |
| ADAMTS2 | ENSG00000087116 | 0.00 | 0.00 | 0 | 0 |
| SCG3 | ENSG00000104112 | 0.00 | 0.00 | 0 | 0 |
| RYR1 | ENSG00000196218 | 0.54 | 0.00 | 1 | 0 |
| COL16A1 | ENSG00000084636 | 0.00 | 0.00 | 0 | 0 |
| ADAMTS17 | ENSG00000140470 | 1.62 | 0.00 | 6 | 0 |
| PDIA4 | ENSG00000155660 | 0.11 | 0.31 | 1 | 2 |
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