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 |
| BPIFA1 | ENSG00000198183 | 0.00 | 0.00 | 0 | 0 |
| CAPN6 | ENSG00000077274 | 0.00 | 0.00 | 0 | 0 |
| FLT3LG | ENSG00000090554 | 0.00 | 0.31 | 0 | 1 |
| DNMT3A | ENSG00000119772 | 0.17 | 0.12 | 1 | 1 |
| RNGTT | ENSG00000111880 | 0.00 | 0.24 | 0 | 2 |
| CHI3L1 | ENSG00000133048 | 0.00 | 0.00 | 0 | 0 |
| BRSK1 | ENSG00000160469 | 0.17 | 0.29 | 1 | 2 |
| GPR153 | ENSG00000158292 | 0.00 | 1.20 | 0 | 6 |
| GALNT2 | ENSG00000143641 | 0.39 | 0.23 | 2 | 1 |
| FSTL1 | ENSG00000163430 | 0.00 | 0.00 | 0 | 0 |
| KCNN3 | ENSG00000143603 | 0.00 | 0.00 | 0 | 0 |
| F8 | ENSG00000185010 | 0.81 | 0.00 | 3 | 0 |
| PTPN23 | ENSG00000076201 | 0.00 | 0.90 | 0 | 5 |
| SYNJ1 | ENSG00000159082 | 0.00 | 0.00 | 0 | 0 |
| GAS6 | ENSG00000183087 | 1.29 | 0.00 | 6 | 0 |
| SEMA3F | ENSG00000001617 | 0.00 | 0.35 | 0 | 2 |
| ADAMTS16 | ENSG00000145536 | 0.00 | 0.00 | 0 | 0 |
| CD1A | ENSG00000158477 | 0.00 | 0.00 | 0 | 0 |
| NTRK2 | ENSG00000148053 | 0.00 | 0.00 | 0 | 0 |
| IL21R | ENSG00000103522 | 0.00 | 0.00 | 0 | 0 |
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