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 |
| LECT1 | ENSG00000136110 | 0.00 | 0.00 | 0 | 0 |
| THSD1 | ENSG00000136114 | 0.00 | 0.00 | 0 | 0 |
| ITM2B | ENSG00000136156 | 0.00 | 0.93 | 0 | 4 |
| EDNRB | ENSG00000136160 | 0.00 | 0.00 | 0 | 0 |
| IL6 | ENSG00000136244 | 0.00 | 0.00 | 0 | 0 |
| ALPK3 | ENSG00000136383 | 0.00 | 0.00 | 0 | 0 |
| CHAD | ENSG00000136457 | 0.00 | 0.00 | 0 | 0 |
| CSH1 | ENSG00000136488 | 0.00 | 0.00 | 0 | 0 |
| EPRS | ENSG00000136628 | 0.00 | 0.33 | 0 | 2 |
| IL10 | ENSG00000136634 | 0.00 | 0.00 | 0 | 0 |
| IL36G | ENSG00000136688 | 0.00 | 0.00 | 0 | 0 |
| IL1RN | ENSG00000136689 | 0.00 | 0.00 | 0 | 0 |
| IL36RN | ENSG00000136695 | 0.00 | 0.00 | 0 | 0 |
| IL36B | ENSG00000136696 | 0.00 | 0.00 | 0 | 0 |
| IL1F10 | ENSG00000136697 | 0.00 | 0.00 | 0 | 0 |
| CFC1 | ENSG00000136698 | 0.00 | 0.00 | 0 | 0 |
| SMPD4 | ENSG00000136699 | 0.00 | 0.12 | 0 | 1 |
| GYPC | ENSG00000136732 | 0.00 | 0.00 | 0 | 0 |
| CDK9 | ENSG00000136807 | 0.00 | 0.11 | 0 | 1 |
| TXN | ENSG00000136810 | 0.00 | 0.15 | 0 | 1 |
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