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 |
| FNTB | ENSG00000257365 | 0.00 | 0.72 | 0 | 3 |
| SLC20A1 | ENSG00000144136 | 0.00 | 0.00 | 0 | 0 |
| RDH13 | ENSG00000160439 | 0.63 | 0.10 | 3 | 1 |
| SLCO2A1 | ENSG00000174640 | 0.00 | 0.00 | 0 | 0 |
| SCYL1 | ENSG00000142186 | 0.18 | 0.00 | 1 | 0 |
| LDHB | ENSG00000111716 | 0.62 | 0.00 | 1 | 0 |
| RSPO3 | ENSG00000146374 | 0.00 | 0.25 | 0 | 2 |
| THBS3 | ENSG00000169231 | 0.78 | 0.00 | 4 | 0 |
| SLC24A2 | ENSG00000155886 | 0.00 | 0.00 | 0 | 0 |
| RARA | ENSG00000131759 | 0.00 | 0.17 | 0 | 1 |
| PAK7 | ENSG00000101349 | 0.00 | 0.00 | 0 | 0 |
| CYP4Z1 | ENSG00000186160 | 0.00 | 0.00 | 0 | 0 |
| SLC16A7 | ENSG00000118596 | 0.00 | 0.00 | 0 | 0 |
| DUSP22 | ENSG00000112679 | 0.39 | 0.39 | 2 | 2 |
| MARK1 | ENSG00000116141 | 0.00 | 0.00 | 0 | 0 |
| SLC35E4 | ENSG00000100036 | 0.23 | 0.00 | 1 | 0 |
| PTGIS | ENSG00000124212 | 0.00 | 0.00 | 0 | 0 |
| USP19 | ENSG00000172046 | 0.00 | 1.06 | 0 | 6 |
| NMT1 | ENSG00000136448 | 0.00 | 0.18 | 0 | 1 |
| PLTP | ENSG00000100979 | 0.13 | 0.00 | 1 | 0 |
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