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 |
| IGHG2 | ENSG00000211893 | 0.00 | 0.00 | 0 | 0 |
| IGHG1 | ENSG00000211896 | 0.00 | 0.00 | 0 | 0 |
| IGHD | ENSG00000211898 | 0.00 | 0.00 | 0 | 0 |
| IGHM | ENSG00000211899 | 0.00 | 0.00 | 0 | 0 |
| IGHV1-2 | ENSG00000211934 | 0.00 | 0.14 | 0 | 1 |
| IGHV3-23 | ENSG00000211949 | 0.00 | 0.14 | 0 | 1 |
| IGHV1-46 | ENSG00000211962 | 0.00 | 0.00 | 0 | 0 |
| TSSK1B | ENSG00000212122 | 0.00 | 0.00 | 0 | 0 |
| TAS2R19 | ENSG00000212124 | 0.55 | 0.00 | 1 | 0 |
| TAS2R50 | ENSG00000212126 | 0.00 | 0.00 | 0 | 0 |
| TAS2R14 | ENSG00000212127 | 0.55 | 0.16 | 1 | 1 |
| TAS2R13 | ENSG00000212128 | 0.00 | 0.00 | 0 | 0 |
| OR2A42 | ENSG00000212807 | 0.00 | 0.00 | 0 | 0 |
| KLK9 | ENSG00000213022 | 0.00 | 0.00 | 0 | 0 |
| CGB8 | ENSG00000213030 | 0.00 | 0.00 | 0 | 0 |
| ACKR1 | ENSG00000213088 | 0.00 | 0.00 | 0 | 0 |
| KLHL23 | ENSG00000213160 | 0.00 | 0.00 | 0 | 0 |
| ASIC3 | ENSG00000213199 | 0.00 | 0.00 | 0 | 0 |
| OR2F1 | ENSG00000213215 | 0.00 | 0.00 | 0 | 0 |
| CSH2 | ENSG00000213218 | 0.00 | 0.00 | 0 | 0 |
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