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 |
| TXNRD1 | ENSG00000198431 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.02 | 0.06 | 0.03 | 0.00 | 0.00 | 0.05 | 0.02 | 0.02 | 0.05 | 0.02 | 0.05 | 0.02 | 0.03 | 0.05 | 0.05 | 0.06 | 0.03 | 0.00 | 0.02 | 0.01 | 0.04 | 0.00 | 0.06 | 0.03 | 0.04 | 0.00 | 0.22 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.08 | 0.07 | 0.22 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.11 | 0.15 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 |
| RPS6KA3 | ENSG00000177189 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.10 | 0.03 | 0.02 | 0.02 | 0.09 | 0.05 | 0.04 | 0.02 | 0.00 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.02 | 0.10 | 0.15 | 0.07 | 0.00 | 0.04 | 0.02 | 0.06 | 0.09 | 0.16 | 0.04 | 0.07 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 |
| C3 | ENSG00000125730 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.08 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.06 | 0.04 | 0.09 | 0.02 | 0.09 | 0.02 | 0.11 | 0.02 | 0.09 | 0.03 | 0.03 | 0.01 | 0.06 | 0.00 | 0.05 | 0.01 | 0.12 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.08 | 0.15 | 0.54 | 0.03 | 0.17 | 0.02 | 0.21 | 0.02 | 0.56 | 0.22 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.05 | 0.05 | 0.03 |
| CDYL2 | ENSG00000166446 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.08 | 0.00 | 0.24 | 0.11 | 0.05 | 0.00 | 0.00 | 0.00 | 0.19 | 0.03 | 0.09 | 0.04 | 0.06 | 0.03 | 0.04 | 0.05 | 0.04 | 0.04 | 0.04 | 0.02 | 0.02 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.06 | 0.05 | 0.01 | 0.05 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.03 | 0.07 | 0.05 | 0.33 | 0.02 | 0.04 | 0.02 | 0.09 | 0.01 | 0.24 | 0.04 | 0.04 | 0.00 | 0.12 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.00 | 0.02 | 0.01 | 0.07 |
| PAM | ENSG00000145730 | 0.12 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.19 | 0.04 | 0.08 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.07 | 0.00 | 0.08 | 0.00 | 0.07 | 0.03 | 0.10 | 0.02 | 0.13 | 0.00 | 0.13 | 0.02 | 0.09 | 0.00 | 0.05 | 0.04 | 0.04 | 0.00 | 0.02 | 0.07 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.07 | 0.08 | 0.45 | 0.00 | 0.06 | 0.01 | 0.05 | 0.01 | 0.14 | 0.11 | 0.04 | 0.01 | 0.00 | 0.00 | 0.07 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.05 |
| USP15 | ENSG00000135655 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.02 | 0.08 | 0.03 | 0.08 | 0.02 | 0.07 | 0.04 | 0.13 | 0.03 | 0.01 | 0.01 | 0.04 | 0.06 | 0.01 | 0.02 | 0.02 | 0.01 | 0.13 | 0.01 | 0.32 | 0.04 | 0.05 | 0.05 | 0.00 | 0.00 | 0.11 | 0.03 | 0.13 | 0.05 | 0.03 | 0.01 | 0.03 | 0.01 | 0.19 | 0.04 | 0.29 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.03 | 0.02 | 0.08 | 0.07 | 0.00 | 0.00 | 0.06 | 0.03 |
| NR4A2 | ENSG00000153234 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.06 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.05 | 0.01 | 0.08 | 0.02 | 0.07 | 0.02 | 0.08 | 0.03 | 0.05 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 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 | 0.03 | 0.01 | 0.04 | 0.01 | 0.01 | 0.00 | 0.08 | 0.05 | 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 |
| MAP2K3 | ENSG00000034152 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.16 | 0.07 | 0.03 | 0.01 | 0.01 | 0.02 | 0.08 | 0.04 | 0.10 | 0.06 | 0.02 | 0.05 | 0.05 | 0.11 | 0.01 | 0.07 | 0.07 | 0.03 | 0.03 | 0.08 | 0.04 | 0.01 | 0.07 | 0.04 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.12 | 0.05 | 0.05 | 0.13 | 0.05 | 0.05 | 0.09 | 0.06 | 0.13 | 0.19 | 0.67 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.02 |
| ROCK2 | ENSG00000134318 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.06 | 0.03 | 0.01 | 0.11 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 | 0.05 | 0.02 | 0.09 | 0.05 | 0.02 | 0.04 | 0.06 | 0.06 | 0.05 | 0.04 | 0.01 | 0.01 | 0.02 | 0.03 | 0.01 | 0.03 | 0.15 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.06 | 0.25 | 0.17 | 0.08 | 0.01 | 0.10 | 0.03 | 0.28 | 0.08 | 0.05 | 0.12 | 0.16 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.03 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.01 | 0.04 |
| SUOX | ENSG00000139531 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.09 | 0.03 | 0.19 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.08 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.28 | 0.04 | 0.03 | 0.00 | 0.21 | 0.00 | 0.39 | 0.07 | 0.19 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.03 | 0.01 | 0.03 | 0.04 | 0.04 | 0.00 | 0.00 | 0.05 | 0.03 |
| NR4A3 | ENSG00000119508 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.02 | 0.06 | 0.02 | 0.04 | 0.05 | 0.02 | 0.04 | 0.01 | 0.07 | 0.02 | 0.02 | 0.04 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.08 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 | 0.06 | 0.16 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.10 | 0.03 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| FGR | ENSG00000000938 | 0.00 | 0.06 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.09 | 0.00 | 0.01 | 0.05 | 0.19 | 0.04 | 0.06 | 0.04 | 0.09 | 0.03 | 0.06 | 0.05 | 0.12 | 0.02 | 0.13 | 0.00 | 0.17 | 0.00 | 0.22 | 0.00 | 0.09 | 0.00 | 0.21 | 0.00 | 1.06 | 0.03 | 0.04 | 0.01 | 0.08 | 0.00 | 0.00 | 0.02 | 0.18 | 0.12 | 0.43 | 0.04 | 0.07 | 0.05 | 0.11 | 0.04 | 0.18 | 0.12 | 0.09 | 0.04 | 0.04 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.02 | 0.02 | 0.08 | 0.00 | 0.07 | 0.08 | 0.05 |
| SLC38A11 | ENSG00000169507 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.11 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.08 | 0.01 | 0.11 | 0.03 | 0.09 | 0.01 | 0.11 | 0.04 | 0.03 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.06 | 0.05 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.30 | 0.05 | 0.05 | 0.01 | 0.05 | 0.01 | 0.09 | 0.00 | 0.05 | 0.09 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| APH1A | ENSG00000117362 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.54 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.43 | 0.00 | 0.31 | 0.00 | 0.09 | 0.01 | 0.23 | 0.00 | 0.22 | 0.00 | 0.03 | 0.00 | 0.17 | 0.00 | 0.06 | 0.00 | 0.37 | 0.00 | 0.43 | 0.01 | 0.24 | 0.00 | 0.11 | 0.00 | 0.00 | 0.00 | 0.42 | 0.01 | 0.68 | 0.02 | 0.19 | 0.00 | 0.28 | 0.00 | 0.54 | 0.00 | 0.43 | 0.02 | 0.14 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.21 | 0.00 |
| ZMYND8 | ENSG00000101040 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.09 | 0.01 | 0.01 | 0.01 | 0.07 | 0.00 | 0.17 | 0.01 | 0.13 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.05 | 0.01 | 0.08 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.18 | 0.02 | 0.44 | 0.03 | 0.02 | 0.04 | 0.19 | 0.01 | 0.40 | 0.00 | 0.13 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 |
| PKN3 | ENSG00000160447 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.06 | 0.03 | 0.06 | 0.02 | 0.11 | 0.02 | 0.10 | 0.02 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.07 | 0.01 | 0.09 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.09 | 0.20 | 0.04 | 0.01 | 0.05 | 0.05 | 0.07 | 0.11 | 0.04 | 0.08 | 0.02 | 0.06 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 |
| SLC5A8 | ENSG00000256870 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.01 | 0.07 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.05 | 0.01 | 0.04 | 0.02 | 0.03 | 0.04 | 0.05 | 0.04 | 0.03 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.06 | 0.03 | 0.04 | 0.00 | 0.22 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.07 | 0.06 | 0.22 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.11 | 0.28 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.08 |
| FER | ENSG00000151422 | 0.17 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.15 | 0.02 | 0.08 | 0.00 | 0.01 | 0.00 | 0.08 | 0.01 | 0.08 | 0.00 | 0.09 | 0.00 | 0.07 | 0.03 | 0.13 | 0.03 | 0.15 | 0.00 | 0.13 | 0.01 | 0.10 | 0.00 | 0.04 | 0.06 | 0.04 | 0.00 | 0.02 | 0.16 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.06 | 0.10 | 0.40 | 0.00 | 0.06 | 0.01 | 0.04 | 0.01 | 0.15 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.08 | 0.04 | 0.02 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.05 |
| RBCK1 | ENSG00000125826 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.05 | 0.14 | 0.03 | 0.03 | 0.03 | 0.10 | 0.03 | 0.05 | 0.02 | 0.04 | 0.05 | 0.09 | 0.09 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.03 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.08 | 0.33 | 0.10 | 0.03 | 0.03 | 0.07 | 0.03 | 0.11 | 0.10 | 0.08 | 0.09 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.04 |
| CYP11A1 | ENSG00000140459 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.05 | 0.02 | 0.06 | 0.02 | 0.02 | 0.03 | 0.08 | 0.03 | 0.05 | 0.03 | 0.02 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.18 | 0.14 | 0.12 | 0.01 | 0.04 | 0.04 | 0.21 | 0.03 | 0.06 | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.12 | 0.01 |
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