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 |
| BRD2 | ENSG00000204256 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.01 | 0.04 | 0.05 | 0.02 | 0.04 | 0.15 | 0.04 | 0.07 | 0.04 | 0.03 | 0.02 | 0.06 | 0.02 | 0.03 | 0.01 | 0.08 | 0.01 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.28 | 0.06 | 0.09 | 0.01 | 0.05 | 0.01 | 0.05 | 0.01 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.20 | 0.01 | 0.00 | 0.01 | 0.01 | 0.11 | 0.00 | 0.11 | 0.01 |
| SLC14A2 | ENSG00000132874 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.04 | 0.06 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 | 0.06 | 0.09 | 0.11 | 0.02 | 0.08 | 0.05 | 0.17 | 0.14 | 0.04 | 0.11 | 0.01 | 0.07 | 0.01 | 0.02 | 0.01 | 0.08 | 0.02 | 0.05 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.18 | 0.17 | 0.01 | 0.02 | 0.06 | 0.03 | 0.27 | 0.00 | 0.11 | 0.06 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.04 | 0.02 |
| VSTM1 | ENSG00000189068 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.17 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.02 | 0.06 | 0.10 | 0.09 | 0.04 | 0.02 | 0.10 | 0.03 | 0.10 | 0.03 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.04 | 0.06 | 0.02 | 0.00 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.16 | 0.03 | 0.13 | 0.26 | 0.13 | 0.06 | 0.06 | 0.05 | 0.35 | 0.10 | 0.09 | 0.16 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.17 | 0.02 | 0.11 | 0.00 | 0.00 | 0.04 | 0.03 |
| MTRR | ENSG00000124275 | 0.01 | 0.00 | 0.01 | 0.01 | 0.03 | 0.09 | 0.02 | 0.02 | 0.20 | 0.02 | 0.00 | 0.01 | 0.06 | 0.01 | 0.29 | 0.01 | 0.31 | 0.01 | 0.09 | 0.02 | 0.18 | 0.02 | 0.09 | 0.02 | 0.02 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.08 | 0.02 | 0.00 | 0.05 | 0.21 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.35 | 0.04 | 0.13 | 0.01 | 0.09 | 0.01 | 0.08 | 0.03 | 0.19 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.02 | 0.00 | 0.02 | 0.15 | 0.08 |
| AMHR2 | ENSG00000135409 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.01 | 0.04 | 0.02 | 0.01 | 0.03 | 0.05 | 0.05 | 0.06 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.14 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.10 | 0.06 | 0.04 | 0.00 | 0.08 | 0.01 | 0.30 | 0.06 | 0.06 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.02 | 0.06 |
| RDH8 | ENSG00000080511 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.08 | 0.04 | 0.00 | 0.01 | 0.14 | 0.01 | 0.03 | 0.04 | 0.07 | 0.06 | 0.05 | 0.05 | 0.04 | 0.06 | 0.03 | 0.05 | 0.01 | 0.01 | 0.01 | 0.04 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.01 | 0.15 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.04 | 0.53 | 0.21 | 0.11 | 0.06 | 0.17 | 0.11 | 0.64 | 0.23 | 0.34 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 |
| RSPRY1 | ENSG00000159579 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.03 | 0.00 | 0.01 | 0.05 | 0.03 | 0.03 | 0.02 | 0.03 | 0.02 | 0.09 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.07 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.04 | 0.05 | 0.14 | 0.00 | 0.07 | 0.04 | 0.06 | 0.05 | 0.12 | 0.03 | 0.06 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.04 |
| IPP | ENSG00000197429 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 | 0.09 | 0.03 | 0.00 | 0.00 | 0.11 | 0.03 | 0.09 | 0.03 | 0.08 | 0.02 | 0.06 | 0.02 | 0.04 | 0.01 | 0.03 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.02 | 0.08 | 0.00 | 0.23 | 0.02 | 0.03 | 0.01 | 0.11 | 0.00 | 0.00 | 0.06 | 0.05 | 0.39 | 0.06 | 0.08 | 0.01 | 0.08 | 0.02 | 0.17 | 0.03 | 0.11 | 0.04 | 0.06 | 0.03 | 0.02 | 0.00 | 0.04 | 0.03 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.07 | 0.02 |
| KCNT1 | ENSG00000107147 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.03 | 0.07 | 0.02 | 0.08 | 0.03 | 0.15 | 0.02 | 0.12 | 0.02 | 0.04 | 0.01 | 0.08 | 0.04 | 0.01 | 0.00 | 0.06 | 0.05 | 0.06 | 0.01 | 0.12 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.14 | 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 |
| CHRND | ENSG00000135902 | 0.01 | 0.07 | 0.04 | 0.04 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.33 | 0.00 | 0.03 | 0.00 | 0.07 | 0.04 | 0.04 | 0.02 | 0.20 | 0.01 | 0.18 | 0.03 | 0.16 | 0.03 | 0.07 | 0.02 | 0.04 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.06 | 0.05 | 0.01 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.09 | 0.15 | 0.21 | 0.01 | 0.39 | 0.04 | 0.06 | 0.13 | 0.06 | 0.04 | 0.37 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.04 | 0.01 | 0.08 | 0.02 | 0.11 |
| ENOX2 | ENSG00000165675 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.04 | 0.05 | 0.01 | 0.03 | 0.02 | 0.10 | 0.02 | 0.09 | 0.02 | 0.05 | 0.01 | 0.10 | 0.02 | 0.13 | 0.01 | 0.03 | 0.00 | 0.05 | 0.02 | 0.01 | 0.00 | 0.09 | 0.03 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.20 | 0.04 | 0.08 | 0.00 | 0.02 | 0.01 | 0.04 | 0.08 | 0.10 | 0.14 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| FKBP8 | ENSG00000105701 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.04 | 0.05 | 0.01 | 0.03 | 0.03 | 0.11 | 0.02 | 0.05 | 0.02 | 0.14 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.08 | 0.02 | 0.06 | 0.03 | 0.18 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.52 | 0.04 | 0.02 | 0.02 | 0.19 | 0.04 | 0.42 | 0.07 | 0.07 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 |
| ZCWPW2 | ENSG00000206559 | 0.00 | 0.18 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.02 | 0.16 | 0.04 | 0.00 | 0.03 | 0.02 | 0.13 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.05 | 0.03 | 0.05 | 0.03 | 0.06 | 0.01 | 0.03 | 0.04 | 0.02 | 0.02 | 0.02 | 0.04 | 0.01 | 0.00 | 0.16 | 0.05 | 0.01 | 0.02 | 0.15 | 0.00 | 0.00 | 0.06 | 0.05 | 0.12 | 0.19 | 0.03 | 0.02 | 0.04 | 0.03 | 0.12 | 0.09 | 0.16 | 0.02 | 0.05 | 0.04 | 0.00 | 0.01 | 0.04 | 0.06 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.03 | 0.04 |
| DUSP13 | ENSG00000079393 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.07 | 0.11 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.08 | 0.05 | 0.04 | 0.03 | 0.07 | 0.03 | 0.20 | 0.05 | 0.04 | 0.02 | 0.12 | 0.04 | 0.06 | 0.00 | 0.04 | 0.04 | 0.25 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.17 | 0.03 | 0.29 | 0.11 | 0.01 | 0.01 | 0.27 | 0.03 | 0.68 | 0.00 | 0.04 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| GLP2R | ENSG00000065325 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.10 | 0.01 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.06 | 0.02 | 0.03 | 0.01 | 0.02 | 0.03 | 0.05 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.14 | 0.00 | 0.07 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.07 | 0.02 | 0.12 | 0.00 | 0.05 | 0.04 | 0.06 | 0.06 | 0.17 | 0.36 | 0.16 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 |
| PRDM13 | ENSG00000112238 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.33 | 0.01 | 0.09 | 0.00 | 0.01 | 0.00 | 0.09 | 0.01 | 0.05 | 0.01 | 0.04 | 0.02 | 0.03 | 0.04 | 0.10 | 0.04 | 0.08 | 0.00 | 0.03 | 0.01 | 0.04 | 0.02 | 0.03 | 0.02 | 0.07 | 0.00 | 0.11 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.10 | 0.16 | 0.16 | 0.02 | 0.01 | 0.03 | 0.02 | 0.06 | 0.05 | 0.12 | 0.11 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.26 | 0.00 | 0.01 | 0.00 | 0.04 | 0.05 | 0.00 | 0.01 | 0.08 |
| SCN11A | ENSG00000168356 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.13 | 0.04 | 0.00 | 0.02 | 0.02 | 0.29 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.04 | 0.03 | 0.06 | 0.05 | 0.07 | 0.00 | 0.02 | 0.04 | 0.02 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.09 | 0.11 | 0.15 | 0.02 | 0.03 | 0.03 | 0.04 | 0.12 | 0.13 | 0.09 | 0.06 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.04 | 0.05 |
| GH2 | ENSG00000136487 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.26 | 0.01 | 0.02 | 0.00 | 0.12 | 0.00 | 0.14 | 0.01 | 0.20 | 0.01 | 0.07 | 0.02 | 0.21 | 0.02 | 0.11 | 0.02 | 0.07 | 0.01 | 0.07 | 0.02 | 0.08 | 0.10 | 0.20 | 0.00 | 0.12 | 0.01 | 0.15 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.56 | 0.01 | 0.24 | 0.03 | 0.17 | 0.02 | 0.10 | 0.03 | 0.27 | 0.02 | 0.17 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.24 | 0.01 |
| PLA2G4D | ENSG00000159337 | 0.00 | 0.01 | 0.01 | 0.02 | 0.14 | 0.00 | 0.01 | 0.06 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.36 | 0.00 | 0.10 | 0.01 | 0.09 | 0.02 | 0.05 | 0.03 | 0.05 | 0.00 | 0.08 | 0.01 | 0.09 | 0.00 | 0.05 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.07 | 0.02 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.11 | 0.03 | 0.37 | 0.00 | 0.10 | 0.01 | 0.08 | 0.05 | 0.44 | 0.07 | 0.08 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.15 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.00 | 0.02 | 0.18 |
| AMPD1 | ENSG00000116748 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.32 | 0.02 | 0.14 | 0.02 | 0.17 | 0.00 | 0.16 | 0.14 | 0.19 | 0.04 | 0.08 | 0.00 | 0.07 | 0.05 | 0.07 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.15 | 0.02 | 0.05 | 0.03 | 0.26 | 0.00 | 0.00 | 0.06 | 0.08 | 0.16 | 0.14 | 0.01 | 0.08 | 0.02 | 0.03 | 0.11 | 0.06 | 0.04 | 0.12 | 0.05 | 0.03 | 0.00 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.14 | 0.09 |
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