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 |
| RRM1 | ENSG00000167325 | 0.00 | 0.00 | 0 | 0 |
| PSMD14 | ENSG00000115233 | 0.00 | 0.15 | 0 | 1 |
| SERPINE2 | ENSG00000135919 | 0.00 | 0.19 | 0 | 1 |
| PDGFA | ENSG00000197461 | 0.42 | 0.41 | 3 | 1 |
| SDC1 | ENSG00000115884 | 0.29 | 0.15 | 2 | 1 |
| CDK11A | ENSG00000008128 | 0.00 | 1.62 | 0 | 8 |
| PRKCI | ENSG00000163558 | 3.00 | 0.00 | 7 | 0 |
| CHD4 | ENSG00000111642 | 0.60 | 0.00 | 1 | 0 |
| LIFR | ENSG00000113594 | 0.21 | 0.00 | 1 | 0 |
| PTEN | ENSG00000171862 | 0.00 | 3.37 | 0 | 14 |
| EZH2 | ENSG00000106462 | 0.11 | 0.16 | 1 | 1 |
| EPHB2 | ENSG00000133216 | 0.00 | 0.34 | 0 | 2 |
| ABL1 | ENSG00000097007 | 0.00 | 0.36 | 0 | 2 |
| EIF2AK4 | ENSG00000128829 | 0.00 | 1.33 | 0 | 5 |
| PSMA7 | ENSG00000101182 | 0.51 | 0.00 | 3 | 0 |
| CD19 | ENSG00000177455 | 0.00 | 0.00 | 0 | 0 |
| TUBA1C | ENSG00000167553 | 0.00 | 0.00 | 0 | 0 |
| SLC7A5 | ENSG00000103257 | 0.00 | 0.11 | 0 | 1 |
| P2RY12 | ENSG00000169313 | 0.00 | 0.00 | 0 | 0 |
| REL | ENSG00000162924 | 0.50 | 0.00 | 1 | 0 |
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