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 |
| GPR157 | ENSG00000180758 | 0.00 | 1.51 | 0 | 4 |
| EIF2AK1 | ENSG00000086232 | 0.59 | 0.41 | 4 | 1 |
| DPF1 | ENSG00000011332 | 0.56 | 0.00 | 1 | 0 |
| SPN | ENSG00000197471 | 0.00 | 0.00 | 0 | 0 |
| EFEMP1 | ENSG00000115380 | 0.00 | 0.00 | 0 | 0 |
| ITK | ENSG00000113263 | 0.00 | 0.12 | 0 | 1 |
| CD44 | ENSG00000026508 | 0.80 | 0.00 | 4 | 0 |
| DERL1 | ENSG00000136986 | 1.48 | 0.00 | 5 | 0 |
| ACPP | ENSG00000014257 | 0.00 | 0.00 | 0 | 0 |
| KLHL22 | ENSG00000099910 | 0.29 | 0.00 | 1 | 0 |
| CA4 | ENSG00000167434 | 0.28 | 0.00 | 1 | 0 |
| ITPKA | ENSG00000137825 | 0.00 | 0.31 | 0 | 2 |
| ATP11A | ENSG00000068650 | 1.38 | 0.00 | 6 | 0 |
| ACP6 | ENSG00000162836 | 0.66 | 0.28 | 2 | 2 |
| GPRC5A | ENSG00000013588 | 0.00 | 0.00 | 0 | 0 |
| LEPR | ENSG00000116678 | 0.00 | 0.00 | 0 | 0 |
| PIK3C2G | ENSG00000139144 | 0.00 | 0.00 | 0 | 0 |
| CCDC80 | ENSG00000091986 | 0.00 | 0.00 | 0 | 0 |
| UGGT1 | ENSG00000136731 | 0.00 | 0.00 | 0 | 0 |
| EPHA7 | ENSG00000135333 | 0.00 | 0.00 | 0 | 0 |
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