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 |
| USP2 | ENSG00000036672 | 0.00 | 0.66 | 0 | 3 |
| MAPK15 | ENSG00000181085 | 0.93 | 0.00 | 3 | 0 |
| SPOCK2 | ENSG00000107742 | 0.00 | 0.00 | 0 | 0 |
| HHAT | ENSG00000054392 | 0.00 | 0.37 | 0 | 2 |
| SIRT5 | ENSG00000124523 | 0.67 | 0.30 | 3 | 2 |
| GABRA3 | ENSG00000011677 | 0.00 | 0.00 | 0 | 0 |
| ATP8A1 | ENSG00000124406 | 0.00 | 0.00 | 0 | 0 |
| SLC16A5 | ENSG00000170190 | 0.00 | 0.00 | 0 | 0 |
| LTBP1 | ENSG00000049323 | 0.00 | 0.00 | 0 | 0 |
| BRD1 | ENSG00000100425 | 0.00 | 1.57 | 0 | 7 |
| ITGB4 | ENSG00000132470 | 0.23 | 0.00 | 1 | 0 |
| SYNJ2 | ENSG00000078269 | 0.00 | 0.60 | 0 | 2 |
| GPR39 | ENSG00000183840 | 0.00 | 0.18 | 0 | 1 |
| SREBF2 | ENSG00000198911 | 0.00 | 0.23 | 0 | 1 |
| PSMB7 | ENSG00000136930 | 0.00 | 0.16 | 0 | 1 |
| P4HTM | ENSG00000178467 | 0.00 | 0.84 | 0 | 5 |
| USP14 | ENSG00000101557 | 0.19 | 0.11 | 1 | 1 |
| LAMA4 | ENSG00000112769 | 0.00 | 0.00 | 0 | 0 |
| GPC3 | ENSG00000147257 | 0.00 | 0.00 | 0 | 0 |
| VIM | ENSG00000026025 | 0.00 | 0.00 | 0 | 0 |
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