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 |
| IGFBP6 | ENSG00000167779 | 0.00 | 0.00 | 0 | 0 |
| ST3GAL3 | ENSG00000126091 | 0.00 | 0.00 | 0 | 0 |
| GRK4 | ENSG00000125388 | 0.00 | 0.00 | 0 | 0 |
| CYP3A5 | ENSG00000106258 | 0.00 | 0.00 | 0 | 0 |
| CACNA1I | ENSG00000100346 | 0.00 | 0.00 | 0 | 0 |
| STK36 | ENSG00000163482 | 0.00 | 0.82 | 0 | 4 |
| SFTPB | ENSG00000168878 | 0.00 | 0.00 | 0 | 0 |
| BPIFB1 | ENSG00000125999 | 0.00 | 0.00 | 0 | 0 |
| RARB | ENSG00000077092 | 0.00 | 0.00 | 0 | 0 |
| CDK19 | ENSG00000155111 | 0.00 | 0.39 | 0 | 3 |
| TNFRSF13B | ENSG00000240505 | 0.00 | 0.00 | 0 | 0 |
| LRRC4C | ENSG00000148948 | 0.00 | 0.00 | 0 | 0 |
| UHRF2 | ENSG00000147854 | 0.15 | 0.36 | 1 | 2 |
| L3MBTL3 | ENSG00000198945 | 0.00 | 0.13 | 0 | 1 |
| EFEMP2 | ENSG00000172638 | 0.00 | 0.00 | 0 | 0 |
| HTRA1 | ENSG00000166033 | 0.00 | 0.25 | 0 | 2 |
| KDM3B | ENSG00000120733 | 0.29 | 0.13 | 1 | 1 |
| KCNB1 | ENSG00000158445 | 0.00 | 0.00 | 0 | 0 |
| TRPM7 | ENSG00000092439 | 0.00 | 0.00 | 0 | 0 |
| CTSD | ENSG00000117984 | 0.00 | 0.42 | 0 | 3 |
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