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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| KIRC | KIRP | KICH | PRAD | BLCA | THYM | MESO | LUAD | LUSC | HNSC | ESCA | STAD | COAD | READ | PAAD | LIHC | CHOL | ACC | PCPG | THCA | BRCA | OV | CESC | UCEC | UCS | SARC | TGCT | LAML | DLBC | LGG | GBM | UVM | SKCM | |||||||||||||||||||||||||||||||||||
| HGNC Symbol | Ensembl Gene ID | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del | Amp | Del |
| PRL | ENSG00000172179 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.95 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.08 | 0.02 | 0.08 | 0.06 | 0.02 | 0.06 | 0.17 | 0.14 | 0.04 | 0.06 | 0.02 | 0.05 | 0.02 | 0.03 | 0.02 | 0.05 | 0.15 | 0.01 | 0.06 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.17 | 0.03 | 0.46 | 0.04 | 0.09 | 0.06 | 0.05 | 0.02 | 0.21 | 0.02 | 0.05 | 0.10 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.21 | 0.00 | 0.17 | 0.00 |
| USP47 | ENSG00000170242 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.08 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.04 | 0.07 | 0.10 | 0.02 | 0.05 | 0.06 | 0.07 | 0.05 | 0.03 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.04 | 0.01 | 0.00 | 0.03 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.00 | 0.05 | 0.08 | 0.06 | 0.35 | 0.02 | 0.04 | 0.05 | 0.06 | 0.05 | 0.05 | 0.04 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 |
| SLC25A31 | ENSG00000151475 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.08 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.02 | 0.07 | 0.02 | 0.03 | 0.01 | 0.05 | 0.01 | 0.06 | 0.01 | 0.04 | 0.02 | 0.02 | 0.00 | 0.02 | 0.02 | 0.05 | 0.00 | 0.09 | 0.11 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.05 | 0.22 | 0.02 | 0.04 | 0.02 | 0.03 | 0.04 | 0.07 | 0.04 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.03 |
| PIK3C2A | ENSG00000011405 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.01 | 0.02 | 0.08 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.04 | 0.07 | 0.07 | 0.02 | 0.04 | 0.05 | 0.03 | 0.03 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.03 | 0.04 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.06 | 0.05 | 0.00 | 0.00 | 0.07 | 0.05 | 0.03 | 0.24 | 0.01 | 0.04 | 0.05 | 0.05 | 0.01 | 0.04 | 0.06 | 0.07 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| SLC11A2 | ENSG00000110911 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.13 | 0.04 | 0.04 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.04 | 0.03 | 0.01 | 0.09 | 0.01 | 0.31 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.05 | 0.11 | 0.05 | 0.04 | 0.00 | 0.06 | 0.01 | 0.24 | 0.03 | 0.20 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.03 | 0.03 | 0.02 | 0.05 | 0.00 | 0.00 | 0.05 | 0.06 |
| HSD3B2 | ENSG00000203859 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.20 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.03 | 0.12 | 0.10 | 0.16 | 0.04 | 0.16 | 0.14 | 0.10 | 0.04 | 0.06 | 0.02 | 0.04 | 0.05 | 0.03 | 0.15 | 0.01 | 0.04 | 0.04 | 0.05 | 0.04 | 0.12 | 0.03 | 0.04 | 0.25 | 0.00 | 0.00 | 0.13 | 0.05 | 0.22 | 0.10 | 0.07 | 0.06 | 0.04 | 0.02 | 0.10 | 0.06 | 0.11 | 0.11 | 0.03 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.08 | 0.32 | 0.06 |
| LPAR4 | ENSG00000147145 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.02 | 0.03 | 0.01 | 0.07 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.10 | 0.03 | 0.03 | 0.02 | 0.03 | 0.02 | 0.01 | 0.05 | 0.15 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.01 |
| CELA3B | ENSG00000219073 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.09 | 0.00 | 0.01 | 0.04 | 0.23 | 0.05 | 0.06 | 0.05 | 0.11 | 0.03 | 0.07 | 0.03 | 0.10 | 0.07 | 0.12 | 0.00 | 0.16 | 0.00 | 0.21 | 0.01 | 0.08 | 0.01 | 0.22 | 0.00 | 1.06 | 0.09 | 0.04 | 0.01 | 0.10 | 0.00 | 0.00 | 0.03 | 0.19 | 0.12 | 0.44 | 0.05 | 0.09 | 0.07 | 0.13 | 0.27 | 0.19 | 0.17 | 0.10 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.11 | 0.00 | 0.02 | 0.04 | 0.11 | 0.00 | 0.12 | 0.05 | 0.08 |
| APOA5 | ENSG00000110243 | 0.00 | 0.01 | 0.00 | 0.07 | 0.02 | 0.02 | 0.01 | 0.08 | 0.03 | 0.11 | 0.00 | 0.00 | 0.02 | 0.06 | 0.04 | 0.08 | 0.04 | 0.09 | 0.04 | 0.16 | 0.07 | 0.13 | 0.05 | 0.08 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.09 | 0.00 | 0.17 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.24 | 0.13 | 0.17 | 0.04 | 0.29 | 0.03 | 0.05 | 0.11 | 0.18 | 0.03 | 0.20 | 0.01 | 0.14 | 0.02 | 0.00 | 0.11 | 0.01 | 0.04 | 0.01 | 0.03 | 0.01 | 0.00 | 0.07 | 0.00 | 0.27 |
| SGPL1 | ENSG00000166224 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.02 | 0.07 | 0.03 | 0.04 | 0.02 | 0.05 | 0.05 | 0.10 | 0.02 | 0.02 | 0.03 | 0.04 | 0.03 | 0.01 | 0.00 | 0.02 | 0.02 | 0.25 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.03 | 0.14 | 0.11 | 0.00 | 0.01 | 0.06 | 0.04 | 0.11 | 0.03 | 0.03 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 |
| CYP2A7 | ENSG00000198077 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.17 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.11 | 0.03 | 0.29 | 0.07 | 0.03 | 0.02 | 0.05 | 0.05 | 0.07 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.11 | 0.02 | 0.09 | 0.02 | 0.12 | 0.01 | 0.05 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.04 | 0.31 | 0.25 | 0.10 | 0.04 | 0.09 | 0.04 | 0.33 | 0.14 | 0.23 | 0.12 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.07 | 0.02 | 0.08 | 0.00 | 0.00 | 0.02 | 0.02 |
| BTN2A1 | ENSG00000112763 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.21 | 0.03 | 0.00 | 0.01 | 0.02 | 0.05 | 0.08 | 0.01 | 0.07 | 0.06 | 0.02 | 0.04 | 0.11 | 0.10 | 0.06 | 0.05 | 0.03 | 0.02 | 0.05 | 0.03 | 0.02 | 0.04 | 0.10 | 0.01 | 0.06 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.35 | 0.05 | 0.09 | 0.03 | 0.04 | 0.01 | 0.20 | 0.02 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.11 | 0.00 | 0.13 | 0.01 |
| PPIG | ENSG00000138398 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.06 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.10 | 0.02 | 0.08 | 0.01 | 0.10 | 0.02 | 0.04 | 0.04 | 0.01 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.05 | 0.06 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.31 | 0.06 | 0.08 | 0.01 | 0.04 | 0.01 | 0.06 | 0.02 | 0.04 | 0.09 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 |
| KLHL20 | ENSG00000076321 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.32 | 0.02 | 0.02 | 0.00 | 0.10 | 0.05 | 0.13 | 0.00 | 0.21 | 0.01 | 0.04 | 0.00 | 0.21 | 0.02 | 0.11 | 0.01 | 0.04 | 0.00 | 0.12 | 0.00 | 0.05 | 0.00 | 0.22 | 0.00 | 0.17 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 | 0.34 | 0.03 | 0.13 | 0.00 | 0.11 | 0.00 | 0.31 | 0.03 | 0.41 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.30 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.14 | 0.01 |
| MMP26 | ENSG00000167346 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.10 | 0.00 | 0.00 | 0.03 | 0.05 | 0.02 | 0.06 | 0.02 | 0.14 | 0.02 | 0.07 | 0.05 | 0.10 | 0.02 | 0.05 | 0.02 | 0.02 | 0.01 | 0.02 | 0.00 | 0.07 | 0.04 | 0.03 | 0.03 | 0.01 | 0.01 | 0.07 | 0.03 | 0.07 | 0.00 | 0.00 | 0.02 | 0.11 | 0.02 | 0.44 | 0.01 | 0.05 | 0.03 | 0.07 | 0.03 | 0.09 | 0.05 | 0.14 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.10 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 |
| C8A | ENSG00000157131 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.04 | 0.00 | 0.00 | 0.06 | 0.03 | 0.06 | 0.05 | 0.06 | 0.03 | 0.05 | 0.03 | 0.04 | 0.04 | 0.02 | 0.04 | 0.00 | 0.06 | 0.00 | 0.04 | 0.00 | 0.01 | 0.05 | 0.05 | 0.00 | 0.25 | 0.04 | 0.03 | 0.00 | 0.16 | 0.00 | 0.00 | 0.09 | 0.05 | 0.29 | 0.12 | 0.08 | 0.02 | 0.05 | 0.02 | 0.00 | 0.06 | 0.23 | 0.02 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.03 | 0.02 |
| SLC25A17 | ENSG00000100372 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.08 | 0.00 | 0.03 | 0.00 | 0.04 | 0.05 | 0.03 | 0.06 | 0.02 | 0.03 | 0.02 | 0.03 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.05 | 0.04 | 0.02 | 0.04 | 0.01 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.03 | 0.04 | 0.22 | 0.07 | 0.02 | 0.06 | 0.04 | 0.21 | 0.21 | 0.07 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.30 | 0.00 |
| HCRTR1 | ENSG00000121764 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.07 | 0.00 | 0.01 | 0.11 | 0.07 | 0.05 | 0.04 | 0.04 | 0.06 | 0.04 | 0.05 | 0.06 | 0.09 | 0.05 | 0.07 | 0.02 | 0.10 | 0.01 | 0.15 | 0.02 | 0.03 | 0.00 | 0.19 | 0.00 | 0.73 | 0.03 | 0.03 | 0.02 | 0.08 | 0.00 | 0.00 | 0.06 | 0.10 | 0.23 | 0.27 | 0.05 | 0.03 | 0.09 | 0.08 | 0.24 | 0.06 | 0.12 | 0.07 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.07 | 0.05 | 0.06 |
| GPD2 | ENSG00000115159 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.05 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.09 | 0.02 | 0.06 | 0.02 | 0.08 | 0.03 | 0.05 | 0.04 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.05 | 0.06 | 0.00 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.29 | 0.04 | 0.04 | 0.01 | 0.04 | 0.01 | 0.01 | 0.00 | 0.08 | 0.07 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 |
| ASIC2 | ENSG00000108684 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.20 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.07 | 0.01 | 0.05 | 0.06 | 0.04 | 0.03 | 0.19 | 0.06 | 0.18 | 0.02 | 0.06 | 0.02 | 0.07 | 0.01 | 0.09 | 0.02 | 0.05 | 0.04 | 0.12 | 0.01 | 0.01 | 0.10 | 0.00 | 0.14 | 0.00 | 0.00 | 0.14 | 0.11 | 0.07 | 0.21 | 0.02 | 0.03 | 0.08 | 0.07 | 0.11 | 0.13 | 0.05 | 0.17 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.01 | 0.02 | 0.00 | 0.04 | 0.00 | 0.05 | 0.02 | 0.03 |
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