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 |
| CDKL3 | ENSG00000006837 | 0.28 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.05 | 0.01 | 0.04 | 0.06 | 0.05 | 0.01 | 0.09 | 0.01 | 0.04 | 0.02 | 0.04 | 0.01 | 0.04 | 0.07 | 0.05 | 0.09 | 0.01 | 0.24 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.05 | 0.12 | 0.17 | 0.03 | 0.03 | 0.02 | 0.03 | 0.10 | 0.01 | 0.05 | 0.06 | 0.01 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.00 | 0.03 | 0.01 | 0.10 |
| ADAM2 | ENSG00000104755 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.34 | 0.06 | 0.00 | 0.00 | 0.02 | 0.00 | 0.20 | 0.04 | 0.56 | 0.03 | 0.17 | 0.02 | 0.30 | 0.05 | 0.05 | 0.04 | 0.16 | 0.03 | 0.15 | 0.06 | 0.05 | 0.00 | 0.05 | 0.06 | 0.06 | 0.01 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.52 | 0.05 | 0.22 | 0.08 | 0.08 | 0.03 | 0.13 | 0.03 | 0.61 | 0.11 | 0.18 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.03 |
| MMP27 | ENSG00000137675 | 0.02 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.28 | 0.06 | 0.00 | 0.00 | 0.06 | 0.06 | 0.11 | 0.05 | 0.11 | 0.07 | 0.39 | 0.09 | 0.13 | 0.08 | 0.09 | 0.05 | 0.04 | 0.01 | 0.02 | 0.03 | 0.05 | 0.01 | 0.05 | 0.06 | 0.00 | 0.10 | 0.01 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.06 | 0.18 | 0.35 | 0.12 | 0.73 | 0.10 | 0.08 | 0.04 | 0.10 | 0.17 | 0.30 | 0.15 | 0.01 | 0.08 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.12 |
| MYH6 | ENSG00000197616 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.07 | 0.01 | 0.00 | 0.00 | 0.02 | 0.19 | 0.03 | 0.16 | 0.07 | 0.06 | 0.07 | 0.12 | 0.05 | 0.05 | 0.04 | 0.03 | 0.02 | 0.01 | 0.07 | 0.01 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.28 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 | 0.26 | 0.12 | 0.08 | 0.02 | 0.05 | 0.03 | 0.06 | 0.07 | 0.23 | 0.03 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.09 | 0.00 | 0.02 | 0.03 | 0.03 |
| TRPM5 | ENSG00000070985 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.07 | 0.01 | 0.16 | 0.02 | 0.07 | 0.02 | 0.15 | 0.02 | 0.06 | 0.04 | 0.01 | 0.01 | 0.03 | 0.01 | 0.06 | 0.04 | 0.03 | 0.03 | 0.01 | 0.01 | 0.05 | 0.02 | 0.07 | 0.00 | 0.00 | 0.02 | 0.12 | 0.03 | 0.47 | 0.01 | 0.07 | 0.03 | 0.08 | 0.10 | 0.09 | 0.07 | 0.15 | 0.02 | 0.04 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.10 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.05 |
| COLEC10 | ENSG00000184374 | 0.02 | 0.01 | 0.01 | 0.00 | 0.09 | 0.00 | 0.07 | 0.00 | 0.25 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.23 | 0.01 | 0.32 | 0.01 | 0.24 | 0.00 | 0.48 | 0.01 | 0.28 | 0.00 | 0.16 | 0.00 | 0.26 | 0.00 | 0.15 | 0.00 | 0.39 | 0.01 | 0.25 | 0.01 | 0.04 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.54 | 0.02 | 1.24 | 0.04 | 0.17 | 0.00 | 0.16 | 0.01 | 0.34 | 0.00 | 0.19 | 0.05 | 0.05 | 0.02 | 0.02 | 0.00 | 0.21 | 0.00 | 0.19 | 0.00 | 0.02 | 0.01 | 0.53 | 0.00 | 0.17 | 0.01 |
| PRDM12 | ENSG00000130711 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.03 | 0.06 | 0.02 | 0.08 | 0.02 | 0.11 | 0.03 | 0.10 | 0.02 | 0.02 | 0.01 | 0.04 | 0.04 | 0.00 | 0.01 | 0.06 | 0.03 | 0.06 | 0.01 | 0.12 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.07 | 0.23 | 0.08 | 0.01 | 0.02 | 0.06 | 0.06 | 0.11 | 0.07 | 0.10 | 0.03 | 0.04 | 0.00 | 0.00 | 0.05 | 0.02 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.03 | 0.02 | 0.03 |
| ADAM7 | ENSG00000069206 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.22 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.07 | 0.00 | 0.11 | 0.01 | 0.06 | 0.02 | 0.06 | 0.01 | 0.05 | 0.00 | 0.11 | 0.01 | 0.17 | 0.00 | 0.04 | 0.00 | 0.11 | 0.00 | 0.08 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.16 | 0.01 | 0.45 | 0.00 | 0.04 | 0.01 | 0.12 | 0.00 | 0.24 | 0.03 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 |
| CHRNA6 | ENSG00000147434 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.21 | 0.05 | 0.00 | 0.00 | 0.04 | 0.00 | 0.18 | 0.04 | 0.35 | 0.03 | 0.12 | 0.03 | 0.38 | 0.07 | 0.08 | 0.04 | 0.15 | 0.02 | 0.11 | 0.05 | 0.03 | 0.00 | 0.04 | 0.05 | 0.00 | 0.02 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.34 | 0.05 | 0.30 | 0.03 | 0.08 | 0.03 | 0.18 | 0.01 | 0.93 | 0.10 | 0.12 | 0.06 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 |
| LYZL1 | ENSG00000120563 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.03 | 0.05 | 0.00 | 0.01 | 0.02 | 0.05 | 0.05 | 0.02 | 0.05 | 0.01 | 0.02 | 0.02 | 0.06 | 0.01 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.05 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.13 | 0.04 | 0.00 | 0.01 | 0.03 | 0.01 | 0.13 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| PZP | ENSG00000126838 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.07 | 0.04 | 0.09 | 0.12 | 0.01 | 0.11 | 0.03 | 0.07 | 0.02 | 0.07 | 0.09 | 0.02 | 0.02 | 0.04 | 0.03 | 0.01 | 0.07 | 0.03 | 0.05 | 0.14 | 0.05 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.05 | 0.30 | 0.10 | 0.03 | 0.03 | 0.03 | 0.03 | 0.16 | 0.03 | 0.11 | 0.11 | 0.55 | 0.00 | 0.00 | 0.01 | 0.00 | 0.08 | 0.11 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.05 | 0.04 |
| CGA | ENSG00000135346 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.39 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 | 0.01 | 0.06 | 0.10 | 0.03 | 0.02 | 0.03 | 0.03 | 0.06 | 0.02 | 0.09 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.04 | 0.06 | 0.00 | 0.11 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.11 | 0.15 | 0.11 | 0.02 | 0.01 | 0.03 | 0.02 | 0.10 | 0.07 | 0.04 | 0.12 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.22 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.02 | 0.04 |
| PSG1 | ENSG00000231924 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.07 | 0.14 | 0.03 | 0.00 | 0.00 | 0.05 | 0.07 | 0.11 | 0.05 | 0.13 | 0.08 | 0.02 | 0.02 | 0.02 | 0.07 | 0.05 | 0.02 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.03 | 0.04 | 0.03 | 0.12 | 0.01 | 0.14 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.05 | 0.15 | 0.28 | 0.11 | 0.05 | 0.04 | 0.05 | 0.09 | 0.17 | 0.17 | 0.12 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.03 | 0.01 | 0.12 | 0.03 | 0.09 | 0.00 | 0.00 | 0.02 | 0.03 |
| ESRRB | ENSG00000119715 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.06 | 0.05 | 0.00 | 0.01 | 0.00 | 0.06 | 0.03 | 0.06 | 0.05 | 0.03 | 0.05 | 0.01 | 0.06 | 0.03 | 0.03 | 0.04 | 0.00 | 0.03 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.10 | 0.00 | 0.26 | 0.02 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.03 | 0.10 | 0.16 | 0.18 | 0.05 | 0.03 | 0.06 | 0.02 | 0.04 | 0.06 | 0.10 | 0.12 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 |
| ABCA10 | ENSG00000154263 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.22 | 0.00 | 0.02 | 0.00 | 0.13 | 0.00 | 0.16 | 0.00 | 0.19 | 0.01 | 0.07 | 0.02 | 0.24 | 0.03 | 0.13 | 0.03 | 0.05 | 0.01 | 0.07 | 0.03 | 0.05 | 0.10 | 0.23 | 0.01 | 0.12 | 0.01 | 0.15 | 0.12 | 0.02 | 0.01 | 0.00 | 0.00 | 0.43 | 0.02 | 0.27 | 0.03 | 0.16 | 0.03 | 0.10 | 0.01 | 0.34 | 0.02 | 0.21 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.02 | 0.01 | 0.17 | 0.01 | 0.22 | 0.02 |
| CATSPER3 | ENSG00000152705 | 0.28 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.07 | 0.01 | 0.05 | 0.01 | 0.05 | 0.02 | 0.05 | 0.02 | 0.08 | 0.01 | 0.04 | 0.02 | 0.04 | 0.01 | 0.03 | 0.07 | 0.04 | 0.09 | 0.01 | 0.24 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.04 | 0.10 | 0.16 | 0.04 | 0.01 | 0.01 | 0.02 | 0.10 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.10 |
| TECTA | ENSG00000109927 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.02 | 0.02 | 0.08 | 0.03 | 0.11 | 0.00 | 0.00 | 0.11 | 0.04 | 0.05 | 0.09 | 0.05 | 0.08 | 0.04 | 0.15 | 0.04 | 0.14 | 0.05 | 0.07 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.10 | 0.00 | 0.17 | 0.00 | 0.05 | 0.03 | 0.06 | 0.00 | 0.00 | 0.02 | 0.22 | 0.25 | 0.16 | 0.04 | 0.31 | 0.05 | 0.06 | 0.05 | 0.17 | 0.03 | 0.23 | 0.00 | 0.19 | 0.03 | 0.00 | 0.08 | 0.08 | 0.06 | 0.01 | 0.03 | 0.01 | 0.00 | 0.07 | 0.00 | 0.27 |
| GABRR1 | ENSG00000146276 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.36 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.06 | 0.07 | 0.03 | 0.03 | 0.03 | 0.06 | 0.07 | 0.02 | 0.07 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 | 0.06 | 0.00 | 0.11 | 0.13 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.11 | 0.16 | 0.12 | 0.02 | 0.01 | 0.02 | 0.01 | 0.19 | 0.05 | 0.07 | 0.12 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.20 | 0.00 | 0.01 | 0.00 | 0.04 | 0.01 | 0.03 | 0.02 | 0.04 |
| SCN5A | ENSG00000183873 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.14 | 0.04 | 0.00 | 0.03 | 0.02 | 0.28 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.04 | 0.03 | 0.04 | 0.05 | 0.08 | 0.00 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.20 | 0.05 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.09 | 0.11 | 0.16 | 0.02 | 0.04 | 0.03 | 0.04 | 0.12 | 0.13 | 0.08 | 0.06 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.09 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.03 | 0.04 | 0.05 |
| TLL2 | ENSG00000095587 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.12 | 0.02 | 0.10 | 0.00 | 0.02 | 0.00 | 0.16 | 0.01 | 0.03 | 0.02 | 0.07 | 0.00 | 0.06 | 0.04 | 0.08 | 0.01 | 0.10 | 0.00 | 0.09 | 0.00 | 0.07 | 0.01 | 0.03 | 0.03 | 0.06 | 0.16 | 0.14 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.08 | 0.07 | 0.31 | 0.00 | 0.07 | 0.02 | 0.10 | 0.03 | 0.09 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 |
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