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 |
| ICAM3 | ENSG00000076662 | 0.00 | 0.00 | 0 | 0 |
| ITPR3 | ENSG00000096433 | 0.00 | 0.00 | 0 | 0 |
| TRIM33 | ENSG00000197323 | 0.00 | 0.66 | 0 | 4 |
| NTSR2 | ENSG00000169006 | 0.00 | 0.00 | 0 | 0 |
| CYP2C9 | ENSG00000138109 | 0.00 | 0.00 | 0 | 0 |
| CDK10 | ENSG00000185324 | 0.00 | 0.52 | 0 | 4 |
| SPARCL1 | ENSG00000152583 | 0.00 | 0.11 | 0 | 1 |
| KLHL3 | ENSG00000146021 | 0.00 | 0.00 | 0 | 0 |
| CMKLR1 | ENSG00000174600 | 0.00 | 0.00 | 0 | 0 |
| CPVL | ENSG00000106066 | 0.00 | 0.00 | 0 | 0 |
| IFIT1 | ENSG00000185745 | 0.00 | 0.00 | 0 | 0 |
| HSPH1 | ENSG00000120694 | 0.17 | 0.00 | 1 | 0 |
| PPARD | ENSG00000112033 | 0.00 | 0.00 | 0 | 0 |
| FKTN | ENSG00000106692 | 0.00 | 0.15 | 0 | 1 |
| SLC40A1 | ENSG00000138449 | 0.00 | 0.00 | 0 | 0 |
| INPP5A | ENSG00000068383 | 0.00 | 0.26 | 0 | 2 |
| CDC42BPA | ENSG00000143776 | 0.00 | 0.25 | 0 | 1 |
| ST6GAL1 | ENSG00000073849 | 0.00 | 0.00 | 0 | 0 |
| TK2 | ENSG00000166548 | 0.15 | 0.14 | 1 | 1 |
| PIP4K2B | ENSG00000276293 | 0.00 | 0.15 | 0 | 1 |
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