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 |
| ULK1 | ENSG00000177169 | 0.00 | 0.58 | 0 | 3 |
| H6PD | ENSG00000049239 | 0.00 | 1.41 | 0 | 3 |
| CHRM3 | ENSG00000133019 | 0.11 | 0.00 | 1 | 0 |
| GALNS | ENSG00000141012 | 0.00 | 0.52 | 0 | 4 |
| CYP4F2 | ENSG00000186115 | 0.00 | 0.00 | 0 | 0 |
| USP30 | ENSG00000135093 | 0.00 | 0.22 | 0 | 1 |
| JAG1 | ENSG00000101384 | 0.11 | 0.00 | 1 | 0 |
| AMD1 | ENSG00000123505 | 0.00 | 0.26 | 0 | 2 |
| COQ6 | ENSG00000119723 | 0.00 | 0.22 | 0 | 2 |
| SLC38A4 | ENSG00000139209 | 0.00 | 0.00 | 0 | 0 |
| IL1RL2 | ENSG00000115598 | 0.00 | 0.00 | 0 | 0 |
| TRPV6 | ENSG00000165125 | 0.00 | 0.00 | 0 | 0 |
| MARCO | ENSG00000019169 | 0.00 | 0.00 | 0 | 0 |
| KCNJ4 | ENSG00000168135 | 0.00 | 0.00 | 0 | 0 |
| SIGLEC12 | ENSG00000254521 | 0.00 | 0.00 | 0 | 0 |
| CHST7 | ENSG00000147119 | 0.00 | 0.00 | 0 | 0 |
| FGF2 | ENSG00000138685 | 0.00 | 0.00 | 0 | 0 |
| MUC5B | ENSG00000117983 | 0.00 | 0.00 | 0 | 0 |
| THOP1 | ENSG00000172009 | 0.00 | 0.88 | 0 | 2 |
| LGR6 | ENSG00000133067 | 0.00 | 0.00 | 0 | 0 |
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