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 |
| SLC19A2 | ENSG00000117479 | 0.33 | 0.00 | 2 | 0 |
| F3 | ENSG00000117525 | 0.00 | 0.11 | 0 | 1 |
| ABCD3 | ENSG00000117528 | 0.00 | 0.62 | 0 | 3 |
| TNFSF4 | ENSG00000117586 | 0.00 | 0.00 | 0 | 0 |
| NEK2 | ENSG00000117650 | 0.00 | 0.17 | 0 | 1 |
| NENF | ENSG00000117691 | 0.00 | 0.37 | 0 | 2 |
| TXNDC12 | ENSG00000117862 | 0.00 | 0.00 | 0 | 0 |
| MMP8 | ENSG00000118113 | 0.00 | 0.00 | 0 | 0 |
| APOA1 | ENSG00000118137 | 0.00 | 0.11 | 0 | 1 |
| TTR | ENSG00000118271 | 0.00 | 0.00 | 0 | 0 |
| ATP10B | ENSG00000118322 | 0.00 | 0.00 | 0 | 0 |
| CNR1 | ENSG00000118432 | 0.00 | 0.00 | 0 | 0 |
| ALDH8A1 | ENSG00000118514 | 0.00 | 0.11 | 0 | 1 |
| CTGF | ENSG00000118523 | 0.00 | 0.26 | 0 | 2 |
| VAMP8 | ENSG00000118640 | 0.00 | 0.00 | 0 | 0 |
| GHRH | ENSG00000118702 | 0.00 | 0.00 | 0 | 0 |
| OLFM3 | ENSG00000118733 | 0.00 | 0.00 | 0 | 0 |
| ABCG2 | ENSG00000118777 | 0.00 | 0.11 | 0 | 1 |
| EEF2KMT | ENSG00000118894 | 0.00 | 0.12 | 0 | 1 |
| UCHL3 | ENSG00000118939 | 0.00 | 0.41 | 0 | 2 |
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