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 |
| CAMK2B | ENSG00000058404 | 0.00 | 0.00 | 0 | 0 |
| SLC2A13 | ENSG00000151229 | 0.00 | 0.00 | 0 | 0 |
| CAPN13 | ENSG00000162949 | 0.00 | 0.00 | 0 | 0 |
| MPO | ENSG00000005381 | 0.00 | 0.00 | 0 | 0 |
| TRPV4 | ENSG00000111199 | 0.00 | 0.00 | 0 | 0 |
| UMODL1 | ENSG00000177398 | 0.00 | 0.00 | 0 | 0 |
| STK35 | ENSG00000125834 | 0.32 | 0.00 | 1 | 0 |
| CLCA1 | ENSG00000016490 | 0.00 | 0.00 | 0 | 0 |
| PARP10 | ENSG00000178685 | 0.74 | 0.00 | 2 | 0 |
| F13B | ENSG00000143278 | 0.00 | 0.00 | 0 | 0 |
| CD86 | ENSG00000114013 | 0.00 | 0.00 | 0 | 0 |
| PLCE1 | ENSG00000138193 | 0.00 | 0.30 | 0 | 1 |
| F11R | ENSG00000158769 | 0.46 | 0.00 | 2 | 0 |
| CPB1 | ENSG00000153002 | 0.00 | 0.00 | 0 | 0 |
| ART4 | ENSG00000111339 | 0.00 | 0.00 | 0 | 0 |
| TASP1 | ENSG00000089123 | 0.00 | 0.00 | 0 | 0 |
| VRK2 | ENSG00000028116 | 0.00 | 0.00 | 0 | 0 |
| LAMP1 | ENSG00000185896 | 1.64 | 0.00 | 7 | 0 |
| EFNA1 | ENSG00000169242 | 1.25 | 0.00 | 5 | 0 |
| CAPN1 | ENSG00000014216 | 0.15 | 0.00 | 1 | 0 |
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