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 |
| ATP8B4 | ENSG00000104043 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.00 | 0.01 | 0.04 | 0.05 | 0.05 | 0.00 | 0.00 | 0.07 | 0.11 | 0.01 | 0.05 | 0.03 | 0.05 | 0.03 | 0.03 | 0.03 | 0.03 | 0.01 | 0.07 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.09 | 0.06 | 0.22 | 0.01 | 0.10 | 0.00 | 0.07 | 0.08 | 0.26 | 0.13 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.00 | 0.03 | 0.00 | 0.10 | 0.00 | 0.00 | 0.04 | 0.11 |
| TRPM4 | ENSG00000130529 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.04 | 0.10 | 0.04 | 0.02 | 0.10 | 0.05 | 0.07 | 0.03 | 0.01 | 0.03 | 0.02 | 0.04 | 0.03 | 0.05 | 0.04 | 0.04 | 0.00 | 0.07 | 0.18 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.09 | 0.05 | 0.05 | 0.32 | 0.06 | 0.07 | 0.04 | 0.05 | 0.17 | 0.18 | 0.02 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.05 | 0.00 | 0.13 | 0.02 | 0.13 | 0.00 | 0.00 | 0.02 | 0.02 |
| SLC12A7 | ENSG00000113504 | 0.01 | 0.01 | 0.03 | 0.01 | 0.03 | 0.11 | 0.03 | 0.01 | 0.27 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.42 | 0.01 | 0.38 | 0.01 | 0.16 | 0.01 | 0.37 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.06 | 0.02 | 0.03 | 0.01 | 0.28 | 0.02 | 0.00 | 0.05 | 0.81 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.13 | 0.02 | 0.48 | 0.05 | 0.22 | 0.02 | 0.16 | 0.01 | 0.26 | 0.03 | 0.34 | 0.13 | 0.03 | 0.03 | 0.00 | 0.00 | 0.17 | 0.00 | 0.01 | 0.06 | 0.04 | 0.04 | 0.03 | 0.02 | 0.30 | 0.07 |
| AIFM1 | ENSG00000156709 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.05 | 0.05 | 0.01 | 0.03 | 0.02 | 0.09 | 0.02 | 0.10 | 0.02 | 0.06 | 0.01 | 0.10 | 0.02 | 0.12 | 0.01 | 0.03 | 0.00 | 0.04 | 0.01 | 0.01 | 0.00 | 0.09 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.18 | 0.05 | 0.07 | 0.00 | 0.04 | 0.01 | 0.08 | 0.08 | 0.03 | 0.14 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| ADGRF1 | ENSG00000153292 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.12 | 0.02 | 0.17 | 0.04 | 0.07 | 0.02 | 0.29 | 0.03 | 0.20 | 0.01 | 0.05 | 0.00 | 0.11 | 0.01 | 0.02 | 0.00 | 0.10 | 0.00 | 0.00 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.22 | 0.07 | 0.06 | 0.03 | 0.06 | 0.01 | 0.03 | 0.03 | 0.14 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.06 | 0.01 |
| KDM5B | ENSG00000117139 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.07 | 0.02 | 0.00 | 0.10 | 0.00 | 0.12 | 0.00 | 0.09 | 0.01 | 0.06 | 0.01 | 0.15 | 0.06 | 0.05 | 0.02 | 0.04 | 0.00 | 0.06 | 0.03 | 0.00 | 0.00 | 0.21 | 0.01 | 0.18 | 0.02 | 0.04 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.26 | 0.00 | 0.30 | 0.07 | 0.06 | 0.00 | 0.10 | 0.01 | 0.17 | 0.03 | 0.10 | 0.13 | 0.05 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.04 | 0.01 | 0.10 | 0.01 | 0.09 | 0.00 | 0.18 | 0.01 |
| MMP24 | ENSG00000125966 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.01 | 0.17 | 0.01 | 0.14 | 0.00 | 0.07 | 0.01 | 0.05 | 0.00 | 0.11 | 0.00 | 0.16 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 | 0.17 | 0.03 | 0.14 | 0.00 | 0.06 | 0.01 | 0.32 | 0.00 | 0.12 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| PDE2A | ENSG00000186642 | 0.00 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.03 | 0.00 | 0.28 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.13 | 0.01 | 0.24 | 0.02 | 0.37 | 0.03 | 0.88 | 0.02 | 0.13 | 0.02 | 0.02 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.08 | 0.02 | 0.00 | 0.02 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.37 | 0.06 | 0.45 | 0.04 | 0.10 | 0.01 | 0.08 | 0.02 | 0.15 | 0.10 | 0.14 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.24 | 0.01 |
| SIAE | ENSG00000110013 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.02 | 0.02 | 0.06 | 0.03 | 0.10 | 0.00 | 0.00 | 0.11 | 0.06 | 0.05 | 0.09 | 0.04 | 0.11 | 0.04 | 0.14 | 0.05 | 0.16 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.19 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.22 | 0.19 | 0.17 | 0.04 | 0.31 | 0.04 | 0.07 | 0.05 | 0.17 | 0.05 | 0.24 | 0.00 | 0.24 | 0.03 | 0.00 | 0.13 | 0.02 | 0.07 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.00 | 0.26 |
| SLC22A3 | ENSG00000146477 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.04 | 0.02 | 0.08 | 0.00 | 0.02 | 0.00 | 0.19 | 0.02 | 0.06 | 0.08 | 0.05 | 0.03 | 0.04 | 0.09 | 0.04 | 0.06 | 0.06 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.03 | 0.02 | 0.12 | 0.00 | 0.18 | 0.14 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.06 | 0.12 | 0.06 | 0.43 | 0.00 | 0.09 | 0.03 | 0.04 | 0.08 | 0.05 | 0.19 | 0.05 | 0.01 | 0.05 | 0.00 | 0.00 | 0.06 | 0.02 | 0.00 | 0.05 | 0.00 | 0.11 | 0.05 | 0.06 | 0.01 | 0.15 |
| GAD1 | ENSG00000128683 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.05 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.11 | 0.02 | 0.09 | 0.01 | 0.17 | 0.02 | 0.05 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.03 | 0.01 | 0.04 | 0.07 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.36 | 0.04 | 0.09 | 0.01 | 0.06 | 0.01 | 0.03 | 0.00 | 0.04 | 0.11 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 |
| ALDH3A1 | ENSG00000108602 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.15 | 0.06 | 0.02 | 0.01 | 0.00 | 0.02 | 0.08 | 0.04 | 0.10 | 0.04 | 0.03 | 0.03 | 0.06 | 0.08 | 0.04 | 0.05 | 0.02 | 0.03 | 0.01 | 0.06 | 0.07 | 0.01 | 0.09 | 0.04 | 0.09 | 0.01 | 0.08 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.11 | 0.05 | 0.04 | 0.15 | 0.02 | 0.05 | 0.07 | 0.05 | 0.26 | 0.21 | 0.69 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.03 |
| CYP4F11 | ENSG00000171903 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.02 | 0.09 | 0.02 | 0.05 | 0.01 | 0.21 | 0.01 | 0.06 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.09 | 0.03 | 0.00 | 0.03 | 0.32 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.77 | 0.02 | 0.02 | 0.01 | 0.27 | 0.01 | 0.39 | 0.03 | 0.13 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 |
| MMP9 | ENSG00000100985 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.08 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.17 | 0.00 | 0.16 | 0.00 | 0.13 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 | 0.22 | 0.04 | 0.02 | 0.05 | 0.09 | 0.01 | 0.42 | 0.00 | 0.10 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 |
| SMO | ENSG00000128602 | 0.01 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.05 | 0.07 | 0.02 | 0.07 | 0.06 | 0.02 | 0.12 | 0.04 | 0.18 | 0.04 | 0.06 | 0.03 | 0.00 | 0.04 | 0.02 | 0.01 | 0.04 | 0.05 | 0.04 | 0.00 | 0.02 | 0.01 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.37 | 0.04 | 0.03 | 0.07 | 0.05 | 0.05 | 0.11 | 0.14 | 0.11 | 0.02 | 0.02 | 0.03 | 0.00 | 0.06 | 0.02 | 0.11 | 0.11 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.20 | 0.01 |
| CYP2E1 | ENSG00000130649 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.05 | 0.01 | 0.06 | 0.05 | 0.10 | 0.00 | 0.02 | 0.02 | 0.14 | 0.05 | 0.05 | 0.07 | 0.06 | 0.03 | 0.04 | 0.05 | 0.10 | 0.09 | 0.08 | 0.02 | 0.06 | 0.02 | 0.06 | 0.01 | 0.01 | 0.02 | 0.10 | 0.14 | 0.17 | 0.09 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.13 | 0.25 | 0.23 | 0.03 | 0.06 | 0.05 | 0.06 | 0.08 | 0.04 | 0.05 | 0.21 | 0.03 | 0.17 | 0.01 | 0.01 | 0.03 | 0.03 | 0.00 | 0.14 | 0.00 | 0.20 | 0.00 | 0.00 | 0.01 | 0.11 |
| SLC52A2 | ENSG00000185803 | 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 |
| SLC2A5 | ENSG00000142583 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.06 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.06 | 0.06 | 0.07 | 0.11 | 0.05 | 0.08 | 0.11 | 0.09 | 0.10 | 0.08 | 0.02 | 0.14 | 0.00 | 0.20 | 0.05 | 0.07 | 0.03 | 0.30 | 0.00 | 1.10 | 0.07 | 0.23 | 0.01 | 0.11 | 0.00 | 0.00 | 0.03 | 0.19 | 0.24 | 0.36 | 0.04 | 0.10 | 0.08 | 0.11 | 0.01 | 0.27 | 0.18 | 0.22 | 0.08 | 0.11 | 0.02 | 0.01 | 0.00 | 0.07 | 0.00 | 0.06 | 0.02 | 0.27 | 0.00 | 0.10 | 0.06 | 0.12 |
| CHI3L2 | ENSG00000064886 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.32 | 0.01 | 0.14 | 0.01 | 0.15 | 0.00 | 0.13 | 0.02 | 0.13 | 0.03 | 0.07 | 0.00 | 0.06 | 0.05 | 0.07 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.10 | 0.04 | 0.04 | 0.00 | 0.26 | 0.00 | 0.00 | 0.04 | 0.10 | 0.18 | 0.14 | 0.01 | 0.08 | 0.01 | 0.03 | 0.01 | 0.07 | 0.04 | 0.11 | 0.03 | 0.04 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.03 | 0.03 | 0.03 | 0.08 | 0.10 |
| MASP2 | ENSG00000009724 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.07 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.26 | 0.06 | 0.05 | 0.05 | 0.11 | 0.05 | 0.08 | 0.16 | 0.07 | 0.15 | 0.07 | 0.01 | 0.13 | 0.01 | 0.21 | 0.03 | 0.06 | 0.03 | 0.25 | 0.00 | 1.07 | 0.03 | 0.21 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.19 | 0.22 | 0.35 | 0.04 | 0.10 | 0.12 | 0.10 | 0.06 | 0.27 | 0.18 | 0.20 | 0.08 | 0.09 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.04 | 0.05 | 0.14 | 0.00 | 0.07 | 0.06 | 0.11 |
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