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 |
| EPAS1 | ENSG00000116016 | 0.00 | 0.00 | 0 | 0 |
| BRD9 | ENSG00000028310 | 2.81 | 0.13 | 9 | 1 |
| ADAM33 | ENSG00000149451 | 0.29 | 0.00 | 1 | 0 |
| RBKS | ENSG00000171174 | 0.16 | 0.00 | 1 | 0 |
| MASP1 | ENSG00000127241 | 0.00 | 0.00 | 0 | 0 |
| PPWD1 | ENSG00000113593 | 0.00 | 0.15 | 0 | 1 |
| PVRL4 | ENSG00000143217 | 1.16 | 0.00 | 2 | 0 |
| LOXL2 | ENSG00000134013 | 0.00 | 0.23 | 0 | 1 |
| SPNS3 | ENSG00000182557 | 0.00 | 0.12 | 0 | 1 |
| CLSTN1 | ENSG00000171603 | 0.00 | 2.06 | 0 | 6 |
| BMPR1B | ENSG00000138696 | 0.00 | 0.00 | 0 | 0 |
| EPHX1 | ENSG00000143819 | 0.11 | 0.24 | 1 | 1 |
| ALK | ENSG00000171094 | 0.00 | 0.00 | 0 | 0 |
| LGR5 | ENSG00000139292 | 0.00 | 0.00 | 0 | 0 |
| KCNJ15 | ENSG00000157551 | 0.00 | 0.00 | 0 | 0 |
| KLK4 | ENSG00000167749 | 0.23 | 0.00 | 1 | 0 |
| STAT6 | ENSG00000166888 | 0.12 | 0.00 | 1 | 0 |
| PTPRZ1 | ENSG00000106278 | 0.00 | 0.00 | 0 | 0 |
| LAMC2 | ENSG00000058085 | 0.00 | 0.00 | 0 | 0 |
| PLAT | ENSG00000104368 | 0.44 | 0.00 | 1 | 0 |
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