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 |
| HSD3B7 | ENSG00000099377 | 0.11 | 0.00 | 1 | 0 |
| SETD1A | ENSG00000099381 | 0.26 | 0.00 | 2 | 0 |
| AMELY | ENSG00000099721 | 0.00 | 0.00 | 0 | 0 |
| PRKY | ENSG00000099725 | 0.00 | 0.00 | 0 | 0 |
| IGFALS | ENSG00000099769 | 0.00 | 0.00 | 0 | 0 |
| MADCAM1 | ENSG00000099866 | 0.00 | 0.00 | 0 | 0 |
| CECR2 | ENSG00000099954 | 0.00 | 0.13 | 0 | 1 |
| P2RX6 | ENSG00000099957 | 0.00 | 0.00 | 0 | 0 |
| SLC7A4 | ENSG00000099960 | 0.29 | 0.00 | 1 | 0 |
| BCL2L13 | ENSG00000099968 | 0.00 | 0.00 | 0 | 0 |
| OSM | ENSG00000099985 | 0.00 | 0.00 | 0 | 0 |
| GGT5 | ENSG00000099998 | 0.00 | 0.00 | 0 | 0 |
| MAPK1 | ENSG00000100030 | 0.15 | 0.00 | 1 | 0 |
| MFNG | ENSG00000100060 | 0.00 | 0.00 | 0 | 0 |
| PLA2G3 | ENSG00000100078 | 0.00 | 0.00 | 0 | 0 |
| LGALS1 | ENSG00000100097 | 0.00 | 0.00 | 0 | 0 |
| PIK3IP1 | ENSG00000100100 | 0.20 | 0.00 | 1 | 0 |
| GGTLC2 | ENSG00000100121 | 0.00 | 0.00 | 0 | 0 |
| SLC16A8 | ENSG00000100156 | 0.00 | 0.00 | 0 | 0 |
| CYP2D6 | ENSG00000100197 | 0.00 | 0.00 | 0 | 0 |
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