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 |
| TIMP3 | ENSG00000100234 | 0.00 | 0.00 | 0 | 0 |
| LTBR | ENSG00000111321 | 0.58 | 0.00 | 1 | 0 |
| PRKAR2B | ENSG00000005249 | 0.00 | 0.00 | 0 | 0 |
| IL20RA | ENSG00000016402 | 0.00 | 0.14 | 0 | 1 |
| ADAMTSL3 | ENSG00000156218 | 0.00 | 0.00 | 0 | 0 |
| MTM1 | ENSG00000171100 | 0.17 | 0.00 | 1 | 0 |
| SLC30A10 | ENSG00000196660 | 0.00 | 0.00 | 0 | 0 |
| BMP5 | ENSG00000112175 | 0.00 | 0.00 | 0 | 0 |
| MBOAT1 | ENSG00000172197 | 0.00 | 0.15 | 0 | 1 |
| AGTR1 | ENSG00000144891 | 0.00 | 0.00 | 0 | 0 |
| ATP2B2 | ENSG00000157087 | 0.00 | 0.00 | 0 | 0 |
| METAP1D | ENSG00000172878 | 0.00 | 0.00 | 0 | 0 |
| VCL | ENSG00000035403 | 0.00 | 0.00 | 0 | 0 |
| PRPS1 | ENSG00000147224 | 0.00 | 0.00 | 0 | 0 |
| FSTL4 | ENSG00000053108 | 0.00 | 0.00 | 0 | 0 |
| PLBD1 | ENSG00000121316 | 0.00 | 0.00 | 0 | 0 |
| PCK1 | ENSG00000124253 | 0.00 | 0.00 | 0 | 0 |
| PPT1 | ENSG00000131238 | 0.61 | 0.00 | 3 | 0 |
| FCGR2A | ENSG00000143226 | 0.00 | 0.00 | 0 | 0 |
| SFMBT1 | ENSG00000163935 | 0.00 | 0.72 | 0 | 4 |
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