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 |
| PIGF | ENSG00000151665 | 0.12 | 0.00 | 1 | 0 |
| MFSD6 | ENSG00000151690 | 0.13 | 0.00 | 1 | 0 |
| KCNJ1 | ENSG00000151704 | 0.00 | 0.00 | 0 | 0 |
| SLC25A4 | ENSG00000151729 | 0.00 | 1.12 | 0 | 7 |
| SLC35F4 | ENSG00000151812 | 0.00 | 0.00 | 0 | 0 |
| CCL28 | ENSG00000151882 | 0.39 | 0.00 | 2 | 0 |
| TUBA3E | ENSG00000152086 | 0.00 | 0.00 | 0 | 0 |
| CYSLTR2 | ENSG00000152207 | 0.00 | 0.00 | 0 | 0 |
| SUV39H2 | ENSG00000152455 | 0.00 | 0.00 | 0 | 0 |
| TMEM123 | ENSG00000152558 | 0.73 | 0.00 | 3 | 0 |
| GRIA4 | ENSG00000152578 | 0.00 | 0.00 | 0 | 0 |
| DSPP | ENSG00000152591 | 0.00 | 0.00 | 0 | 0 |
| DMP1 | ENSG00000152592 | 0.00 | 0.00 | 0 | 0 |
| MEPE | ENSG00000152595 | 0.00 | 0.00 | 0 | 0 |
| PELO | ENSG00000152684 | 0.00 | 0.00 | 0 | 0 |
| CNTNAP4 | ENSG00000152910 | 0.00 | 0.00 | 0 | 0 |
| MR1 | ENSG00000153029 | 0.00 | 0.00 | 0 | 0 |
| OR14K1 | ENSG00000153230 | 0.00 | 0.00 | 0 | 0 |
| CD8A | ENSG00000153563 | 0.00 | 0.00 | 0 | 0 |
| KCNJ16 | ENSG00000153822 | 0.00 | 0.00 | 0 | 0 |
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