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 |
| ENOX1 | ENSG00000120658 | 0.00 | 0.38 | 0 | 2 |
| JARID2 | ENSG00000008083 | 0.25 | 0.31 | 1 | 2 |
| SCNN1A | ENSG00000111319 | 0.58 | 0.00 | 1 | 0 |
| CHRM1 | ENSG00000168539 | 0.00 | 0.00 | 0 | 0 |
| ATP9B | ENSG00000166377 | 0.00 | 1.76 | 0 | 10 |
| ABCB5 | ENSG00000004846 | 0.00 | 0.00 | 0 | 0 |
| SLCO5A1 | ENSG00000137571 | 0.36 | 0.00 | 2 | 0 |
| CACNG7 | ENSG00000105605 | 0.00 | 0.17 | 0 | 1 |
| FAAH | ENSG00000117480 | 0.00 | 0.00 | 0 | 0 |
| TMEFF2 | ENSG00000144339 | 0.00 | 0.00 | 0 | 0 |
| RPN1 | ENSG00000163902 | 0.00 | 0.00 | 0 | 0 |
| MTA2 | ENSG00000149480 | 0.12 | 0.12 | 1 | 1 |
| NLGN1 | ENSG00000169760 | 0.20 | 0.00 | 1 | 0 |
| SLC47A1 | ENSG00000142494 | 0.81 | 0.00 | 2 | 0 |
| HLA-C | ENSG00000204525 | 0.00 | 0.00 | 0 | 0 |
| SCNN1G | ENSG00000166828 | 0.00 | 0.00 | 0 | 0 |
| TMCO3 | ENSG00000150403 | 1.62 | 0.00 | 7 | 0 |
| GRIK2 | ENSG00000164418 | 0.00 | 0.00 | 0 | 0 |
| EPDR1 | ENSG00000086289 | 0.00 | 0.00 | 0 | 0 |
| SLC8A3 | ENSG00000100678 | 0.00 | 0.11 | 0 | 1 |
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