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 |
| PRDM14 | ENSG00000147596 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.00 | 0.07 | 0.00 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 | 0.10 | 0.02 | 0.06 | 0.01 | 0.08 | 0.00 | 0.11 | 0.01 | 0.06 | 0.00 | 0.13 | 0.03 | 0.01 | 0.01 | 0.10 | 0.00 | 0.05 | 0.02 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.20 | 0.01 | 0.39 | 0.07 | 0.05 | 0.01 | 0.11 | 0.01 | 0.44 | 0.02 | 0.13 | 0.05 | 0.21 | 0.00 | 0.01 | 0.00 | 0.04 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.22 | 0.00 | 0.07 | 0.01 |
| SLC26A7 | ENSG00000147606 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.08 | 0.01 | 0.21 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.15 | 0.01 | 0.15 | 0.02 | 0.08 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.09 | 0.00 | 0.19 | 0.02 | 0.04 | 0.01 | 0.17 | 0.01 | 0.20 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.38 | 0.00 | 0.36 | 0.09 | 0.07 | 0.01 | 0.08 | 0.01 | 0.28 | 0.02 | 0.16 | 0.06 | 0.15 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.06 | 0.01 | 0.02 | 0.01 | 0.36 | 0.00 | 0.10 | 0.01 |
| SLC39A4 | ENSG00000147804 | 0.02 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.05 | 0.03 | 0.19 | 0.03 | 0.02 | 0.00 | 0.10 | 0.05 | 0.25 | 0.02 | 0.36 | 0.02 | 0.28 | 0.01 | 0.42 | 0.02 | 0.20 | 0.02 | 0.15 | 0.03 | 0.25 | 0.03 | 0.13 | 0.01 | 0.35 | 0.01 | 0.25 | 0.01 | 0.10 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.41 | 0.04 | 1.46 | 0.05 | 0.20 | 0.01 | 0.12 | 0.02 | 0.18 | 0.03 | 0.16 | 0.11 | 0.06 | 0.03 | 0.02 | 0.00 | 0.26 | 0.02 | 0.17 | 0.05 | 0.03 | 0.03 | 0.48 | 0.00 | 0.23 | 0.02 |
| CER1 | ENSG00000147869 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.13 | 0.01 | 0.01 | 0.03 | 0.11 | 0.04 | 0.10 | 0.12 | 0.12 | 0.20 | 0.05 | 0.14 | 0.10 | 0.03 | 0.11 | 0.01 | 0.02 | 0.02 | 0.04 | 0.01 | 0.08 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.03 | 0.00 | 0.00 | 0.08 | 0.06 | 0.18 | 0.14 | 0.12 | 0.03 | 0.05 | 0.02 | 0.08 | 0.05 | 0.05 | 0.15 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.09 | 0.04 | 0.23 | 0.00 | 0.00 | 0.03 | 0.10 |
| PLIN2 | ENSG00000147872 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.08 | 0.13 | 0.01 | 0.06 | 0.00 | 0.16 | 0.02 | 0.08 | 0.07 | 0.09 | 0.12 | 0.04 | 0.06 | 0.10 | 0.04 | 0.08 | 0.02 | 0.02 | 0.01 | 0.03 | 0.03 | 0.09 | 0.04 | 0.03 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.14 | 0.12 | 0.06 | 0.03 | 0.05 | 0.02 | 0.04 | 0.05 | 0.09 | 0.14 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.00 | 0.12 | 0.01 | 0.35 | 0.00 | 0.00 | 0.01 | 0.11 |
| IFNA5 | ENSG00000147873 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.06 | 0.01 | 0.05 | 0.10 | 0.44 | 0.00 | 0.04 | 0.00 | 0.76 | 0.03 | 0.28 | 0.04 | 0.37 | 0.06 | 0.18 | 0.02 | 0.29 | 0.01 | 0.22 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.40 | 0.01 | 0.10 | 0.00 | 0.16 | 0.00 | 0.13 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.09 | 0.07 | 0.19 | 0.06 | 0.05 | 0.05 | 0.02 | 0.04 | 0.05 | 0.05 | 0.26 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.26 | 0.01 | 1.83 | 0.00 | 0.00 | 0.01 | 0.32 |
| IFNA16 | ENSG00000147885 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.06 | 0.01 | 0.03 | 0.09 | 0.41 | 0.00 | 0.04 | 0.00 | 0.76 | 0.03 | 0.27 | 0.05 | 0.36 | 0.06 | 0.16 | 0.02 | 0.29 | 0.01 | 0.21 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.37 | 0.01 | 0.10 | 0.00 | 0.16 | 0.00 | 0.13 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.09 | 0.07 | 0.18 | 0.06 | 0.05 | 0.05 | 0.02 | 0.04 | 0.05 | 0.05 | 0.26 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.24 | 0.01 | 1.02 | 0.00 | 0.00 | 0.01 | 0.32 |
| IFNK | ENSG00000147896 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.10 | 0.00 | 0.02 | 0.01 | 0.57 | 0.05 | 0.09 | 0.19 | 0.16 | 0.04 | 0.09 | 0.10 | 0.15 | 0.04 | 0.10 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.11 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.06 | 0.10 | 0.12 | 0.01 | 0.04 | 0.03 | 0.02 | 0.00 | 0.05 | 0.11 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.09 | 0.02 | 0.38 | 0.00 | 0.00 | 0.04 | 0.12 |
| SIGMAR1 | ENSG00000147955 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 | 0.10 | 0.05 | 0.02 | 0.36 | 0.04 | 0.21 | 0.03 | 0.26 | 0.01 | 0.17 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.04 | 0.01 | 0.24 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.09 | 0.06 | 0.01 | 0.01 | 0.04 | 0.02 | 0.01 | 0.05 | 0.11 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.07 | 0.00 | 0.03 | 0.07 | 0.05 |
| C9orf3 | ENSG00000148120 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.06 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.05 | 0.04 | 0.04 | 0.07 | 0.02 | 0.10 | 0.06 | 0.03 | 0.05 | 0.01 | 0.02 | 0.04 | 0.03 | 0.01 | 0.04 | 0.03 | 0.04 | 0.00 | 0.08 | 0.04 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.04 | 0.08 | 0.15 | 0.03 | 0.04 | 0.02 | 0.05 | 0.00 | 0.17 | 0.11 | 0.01 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| OR13C4 | ENSG00000148136 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.04 | 0.05 | 0.00 | 0.01 | 0.02 | 0.05 | 0.03 | 0.02 | 0.06 | 0.00 | 0.05 | 0.00 | 0.08 | 0.01 | 0.03 | 0.03 | 0.00 | 0.01 | 0.04 | 0.04 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.08 | 0.12 | 0.03 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.12 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| CRB2 | ENSG00000148204 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.00 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.06 | 0.03 | 0.06 | 0.02 | 0.11 | 0.01 | 0.08 | 0.02 | 0.01 | 0.02 | 0.04 | 0.03 | 0.00 | 0.01 | 0.03 | 0.04 | 0.06 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.14 | 0.14 | 0.02 | 0.01 | 0.03 | 0.04 | 0.02 | 0.16 | 0.09 | 0.04 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| OR5C1 | ENSG00000148215 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.05 | 0.02 | 0.06 | 0.01 | 0.11 | 0.01 | 0.08 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.06 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.12 | 0.14 | 0.02 | 0.01 | 0.02 | 0.03 | 0.03 | 0.16 | 0.09 | 0.04 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| PTGES | ENSG00000148344 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.04 | 0.03 | 0.06 | 0.02 | 0.06 | 0.02 | 0.11 | 0.03 | 0.12 | 0.02 | 0.01 | 0.01 | 0.04 | 0.03 | 0.01 | 0.01 | 0.05 | 0.03 | 0.06 | 0.01 | 0.10 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.08 | 0.22 | 0.06 | 0.01 | 0.05 | 0.06 | 0.04 | 0.11 | 0.04 | 0.10 | 0.02 | 0.06 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.03 | 0.02 | 0.03 |
| LCN2 | ENSG00000148346 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.05 | 0.03 | 0.06 | 0.01 | 0.13 | 0.02 | 0.12 | 0.02 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.05 | 0.04 | 0.07 | 0.04 | 0.18 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.04 | 0.10 | 0.17 | 0.06 | 0.01 | 0.07 | 0.05 | 0.23 | 0.11 | 0.04 | 0.08 | 0.02 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.00 | 0.02 | 0.04 | 0.02 |
| LCN9 | ENSG00000148386 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.03 | 0.07 | 0.02 | 0.07 | 0.03 | 0.13 | 0.02 | 0.11 | 0.02 | 0.04 | 0.01 | 0.08 | 0.04 | 0.01 | 0.00 | 0.06 | 0.04 | 0.06 | 0.01 | 0.12 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.13 | 0.24 | 0.06 | 0.02 | 0.01 | 0.05 | 0.07 | 0.14 | 0.08 | 0.16 | 0.03 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 |
| SLC39A12 | ENSG00000148482 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.12 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.03 | 0.04 | 0.04 | 0.05 | 0.02 | 0.03 | 0.04 | 0.04 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.20 | 0.05 | 0.02 | 0.02 | 0.05 | 0.01 | 0.20 | 0.00 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.03 |
| RGR | ENSG00000148604 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.00 | 0.01 | 0.06 | 0.02 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.03 | 0.07 | 0.03 | 0.07 | 0.02 | 0.07 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.05 | 0.25 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.05 | 0.13 | 0.21 | 0.02 | 0.04 | 0.07 | 0.06 | 0.02 | 0.08 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 |
| CYP17A1 | ENSG00000148795 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.01 | 0.10 | 0.00 | 0.02 | 0.00 | 0.18 | 0.01 | 0.03 | 0.02 | 0.09 | 0.00 | 0.04 | 0.03 | 0.08 | 0.03 | 0.08 | 0.00 | 0.11 | 0.00 | 0.07 | 0.01 | 0.03 | 0.03 | 0.07 | 0.11 | 0.17 | 0.09 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.09 | 0.08 | 0.32 | 0.01 | 0.07 | 0.02 | 0.08 | 0.05 | 0.11 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.04 |
| GSTO1 | ENSG00000148834 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.10 | 0.00 | 0.02 | 0.01 | 0.20 | 0.01 | 0.04 | 0.02 | 0.08 | 0.00 | 0.04 | 0.04 | 0.07 | 0.05 | 0.08 | 0.00 | 0.10 | 0.01 | 0.08 | 0.01 | 0.03 | 0.01 | 0.07 | 0.11 | 0.17 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.10 | 0.07 | 0.31 | 0.01 | 0.07 | 0.04 | 0.08 | 0.03 | 0.11 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.07 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
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