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 |
| PRKCSH | ENSG00000130175 | 0.00 | 0.00 | 0 | 0 |
| PDGFB | ENSG00000100311 | 0.00 | 0.00 | 0 | 0 |
| PHF10 | ENSG00000130024 | 0.00 | 1.06 | 0 | 4 |
| USP21 | ENSG00000143258 | 0.57 | 0.00 | 3 | 0 |
| PDK2 | ENSG00000005882 | 0.00 | 0.00 | 0 | 0 |
| DNAJC16 | ENSG00000116138 | 0.00 | 1.06 | 0 | 5 |
| ENG | ENSG00000106991 | 0.00 | 0.00 | 0 | 0 |
| PRCP | ENSG00000137509 | 0.22 | 0.00 | 1 | 0 |
| RRM2B | ENSG00000048392 | 0.59 | 0.00 | 2 | 0 |
| CHST10 | ENSG00000115526 | 0.00 | 0.00 | 0 | 0 |
| KLHL12 | ENSG00000117153 | 0.11 | 0.00 | 1 | 0 |
| ATP6V0A1 | ENSG00000033627 | 0.00 | 0.20 | 0 | 1 |
| MATN2 | ENSG00000132561 | 0.00 | 0.00 | 0 | 0 |
| AKAP1 | ENSG00000121057 | 0.00 | 0.00 | 0 | 0 |
| FCGRT | ENSG00000104870 | 0.00 | 0.49 | 0 | 2 |
| HAGH | ENSG00000063854 | 0.00 | 0.00 | 0 | 0 |
| PWWP2B | ENSG00000171813 | 0.00 | 0.25 | 0 | 2 |
| PTGR1 | ENSG00000106853 | 0.00 | 0.15 | 0 | 1 |
| KBTBD2 | ENSG00000170852 | 0.00 | 0.00 | 0 | 0 |
| CLOCK | ENSG00000134852 | 1.29 | 0.00 | 5 | 0 |
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