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 |
| CNTN4 | ENSG00000144619 | 0.00 | 0.00 | 0 | 0 |
| CBX4 | ENSG00000141582 | 1.28 | 0.00 | 5 | 0 |
| SLIT1 | ENSG00000187122 | 0.00 | 0.00 | 0 | 0 |
| PRSS33 | ENSG00000103355 | 0.00 | 0.00 | 0 | 0 |
| ADAM23 | ENSG00000114948 | 0.00 | 0.00 | 0 | 0 |
| SLC38A1 | ENSG00000111371 | 0.00 | 0.00 | 0 | 0 |
| APOH | ENSG00000091583 | 0.00 | 0.00 | 0 | 0 |
| CACNB4 | ENSG00000182389 | 0.00 | 0.00 | 0 | 0 |
| CDKL1 | ENSG00000100490 | 0.00 | 0.00 | 0 | 0 |
| PLCB1 | ENSG00000182621 | 0.00 | 0.00 | 0 | 0 |
| ENPP2 | ENSG00000136960 | 0.00 | 0.00 | 0 | 0 |
| GANAB | ENSG00000089597 | 0.12 | 0.12 | 1 | 1 |
| LAMB1 | ENSG00000091136 | 0.00 | 0.00 | 0 | 0 |
| PTPN1 | ENSG00000196396 | 0.00 | 0.00 | 0 | 0 |
| ABCC2 | ENSG00000023839 | 0.00 | 0.00 | 0 | 0 |
| TNFRSF1A | ENSG00000067182 | 0.58 | 0.00 | 1 | 0 |
| TRPC1 | ENSG00000144935 | 0.00 | 0.00 | 0 | 0 |
| FGF18 | ENSG00000156427 | 0.00 | 0.00 | 0 | 0 |
| SLC23A1 | ENSG00000170482 | 0.29 | 0.00 | 1 | 0 |
| NR1D2 | ENSG00000174738 | 0.00 | 0.34 | 0 | 2 |
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