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 |
| KNG1 | ENSG00000113889 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.04 | 0.19 | 0.01 | 0.00 | 0.00 | 0.02 | 0.07 | 0.14 | 0.05 | 1.58 | 0.00 | 0.61 | 0.00 | 0.70 | 0.02 | 0.22 | 0.01 | 0.04 | 0.01 | 0.06 | 0.02 | 0.03 | 0.00 | 0.15 | 0.02 | 0.12 | 0.03 | 0.10 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.19 | 0.02 | 1.06 | 0.04 | 0.62 | 0.00 | 0.33 | 0.01 | 0.78 | 0.09 | 0.12 | 0.09 | 0.24 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.02 | 0.02 | 0.12 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 |
| GPR158 | ENSG00000151025 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.06 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.04 | 0.02 | 0.03 | 0.03 | 0.02 | 0.06 | 0.03 | 0.05 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.12 | 0.07 | 0.01 | 0.01 | 0.02 | 0.02 | 0.08 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 |
| ME1 | ENSG00000065833 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.32 | 0.04 | 0.09 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.06 | 0.10 | 0.02 | 0.03 | 0.05 | 0.08 | 0.11 | 0.02 | 0.09 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.02 | 0.13 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.10 | 0.12 | 0.11 | 0.02 | 0.01 | 0.02 | 0.01 | 0.03 | 0.06 | 0.05 | 0.12 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.20 | 0.00 | 0.01 | 0.00 | 0.03 | 0.05 | 0.03 | 0.02 | 0.04 |
| SULF1 | ENSG00000137573 | 0.00 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.06 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 | 0.10 | 0.02 | 0.06 | 0.01 | 0.07 | 0.02 | 0.09 | 0.02 | 0.06 | 0.00 | 0.15 | 0.03 | 0.01 | 0.01 | 0.10 | 0.00 | 0.06 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.20 | 0.02 | 0.39 | 0.07 | 0.04 | 0.01 | 0.09 | 0.01 | 0.39 | 0.02 | 0.15 | 0.07 | 0.22 | 0.00 | 0.01 | 0.00 | 0.04 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.23 | 0.00 | 0.06 | 0.01 |
| CLCN6 | ENSG00000011021 | 0.00 | 0.06 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.05 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.07 | 0.05 | 0.05 | 0.12 | 0.04 | 0.08 | 0.17 | 0.08 | 0.10 | 0.08 | 0.01 | 0.13 | 0.00 | 0.20 | 0.03 | 0.06 | 0.03 | 0.23 | 0.00 | 1.07 | 0.04 | 0.13 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.19 | 0.21 | 0.36 | 0.04 | 0.10 | 0.07 | 0.10 | 0.08 | 0.25 | 0.19 | 0.19 | 0.08 | 0.09 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.08 | 0.12 | 0.00 | 0.07 | 0.07 | 0.11 |
| SCUBE2 | ENSG00000175356 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.06 | 0.03 | 0.05 | 0.01 | 0.13 | 0.01 | 0.05 | 0.05 | 0.08 | 0.02 | 0.04 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.04 | 0.04 | 0.02 | 0.03 | 0.01 | 0.01 | 0.04 | 0.02 | 0.07 | 0.00 | 0.00 | 0.03 | 0.10 | 0.02 | 0.39 | 0.01 | 0.05 | 0.03 | 0.07 | 0.03 | 0.10 | 0.03 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.08 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.03 |
| HGF | ENSG00000019991 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.13 | 0.02 | 0.10 | 0.02 | 0.21 | 0.02 | 0.09 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.06 | 0.01 | 0.04 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.15 | 0.07 | 0.04 | 0.01 | 0.02 | 0.02 | 0.08 | 0.03 | 0.09 | 0.05 | 0.08 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 |
| IKBKE | ENSG00000263528 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.06 | 0.06 | 0.01 | 0.00 | 0.07 | 0.02 | 0.13 | 0.01 | 0.09 | 0.01 | 0.06 | 0.01 | 0.17 | 0.08 | 0.07 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.20 | 0.01 | 0.18 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.22 | 0.10 | 0.08 | 0.00 | 0.08 | 0.01 | 0.23 | 0.05 | 0.04 | 0.18 | 0.03 | 0.02 | 0.01 | 0.00 | 0.18 | 0.10 | 0.00 | 0.01 | 0.04 | 0.02 | 0.09 | 0.00 | 0.15 | 0.02 |
| KMO | ENSG00000117009 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.05 | 0.10 | 0.03 | 0.02 | 0.00 | 0.05 | 0.07 | 0.12 | 0.01 | 0.15 | 0.02 | 0.07 | 0.01 | 0.18 | 0.04 | 0.12 | 0.03 | 0.04 | 0.02 | 0.08 | 0.02 | 0.01 | 0.01 | 0.18 | 0.01 | 0.23 | 0.02 | 0.06 | 0.06 | 0.00 | 0.04 | 0.00 | 0.00 | 0.26 | 0.02 | 0.47 | 0.11 | 0.11 | 0.02 | 0.10 | 0.02 | 0.30 | 0.00 | 0.03 | 0.23 | 0.05 | 0.02 | 0.01 | 0.00 | 0.05 | 0.19 | 0.04 | 0.03 | 0.03 | 0.05 | 0.08 | 0.03 | 0.21 | 0.03 |
| SUV420H2 | ENSG00000133247 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.20 | 0.03 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.05 | 0.12 | 0.08 | 0.05 | 0.02 | 0.15 | 0.03 | 0.13 | 0.02 | 0.03 | 0.03 | 0.01 | 0.04 | 0.05 | 0.04 | 0.06 | 0.02 | 0.02 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.17 | 0.03 | 0.15 | 0.26 | 0.14 | 0.06 | 0.06 | 0.05 | 0.36 | 0.10 | 0.04 | 0.19 | 0.00 | 0.06 | 0.01 | 0.00 | 0.26 | 0.03 | 0.00 | 0.19 | 0.03 | 0.12 | 0.00 | 0.00 | 0.03 | 0.05 |
| SEPP1 | ENSG00000250722 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.19 | 0.01 | 0.23 | 0.01 | 0.10 | 0.00 | 0.23 | 0.01 | 0.19 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.04 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.11 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.02 | 0.22 | 0.02 | 0.07 | 0.00 | 0.09 | 0.01 | 0.25 | 0.03 | 0.21 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.12 | 0.03 |
| CLDN18 | ENSG00000066405 | 0.03 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.06 | 0.01 | 0.36 | 0.01 | 0.24 | 0.00 | 0.27 | 0.02 | 0.13 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.06 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.09 | 0.02 | 0.46 | 0.03 | 0.26 | 0.00 | 0.09 | 0.01 | 0.19 | 0.02 | 0.09 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 |
| TENM1 | ENSG00000009694 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.06 | 0.06 | 0.01 | 0.03 | 0.02 | 0.09 | 0.02 | 0.08 | 0.04 | 0.07 | 0.02 | 0.10 | 0.02 | 0.10 | 0.03 | 0.03 | 0.01 | 0.05 | 0.02 | 0.01 | 0.00 | 0.10 | 0.03 | 0.00 | 0.01 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.19 | 0.05 | 0.06 | 0.02 | 0.02 | 0.01 | 0.01 | 0.08 | 0.08 | 0.11 | 0.00 | 0.03 | 0.00 | 0.03 | 0.10 | 0.05 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 |
| ADAM19 | ENSG00000135074 | 0.31 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.09 | 0.04 | 0.04 | 0.01 | 0.05 | 0.01 | 0.04 | 0.05 | 0.02 | 0.02 | 0.05 | 0.01 | 0.02 | 0.03 | 0.03 | 0.02 | 0.02 | 0.09 | 0.02 | 0.09 | 0.01 | 0.21 | 0.02 | 0.01 | 0.04 | 0.01 | 0.00 | 0.04 | 0.03 | 0.17 | 0.14 | 0.03 | 0.02 | 0.02 | 0.02 | 0.05 | 0.02 | 0.07 | 0.06 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.07 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.13 |
| WHSC1 | ENSG00000109685 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.03 | 0.17 | 0.04 | 0.02 | 0.00 | 0.01 | 0.03 | 0.05 | 0.05 | 0.05 | 0.04 | 0.02 | 0.07 | 0.09 | 0.08 | 0.07 | 0.07 | 0.02 | 0.03 | 0.05 | 0.04 | 0.10 | 0.02 | 0.04 | 0.07 | 0.06 | 0.01 | 0.24 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.07 | 0.43 | 0.08 | 0.03 | 0.06 | 0.16 | 0.05 | 1.09 | 0.05 | 0.15 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.05 | 0.02 | 0.02 | 0.00 | 0.07 | 0.05 |
| RBM10 | ENSG00000182872 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.05 | 0.02 | 0.03 | 0.02 | 0.04 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.16 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.39 | 0.06 | 0.03 | 0.03 | 0.14 | 0.01 | 0.42 | 0.04 | 0.17 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 |
| SORD | ENSG00000140263 | 0.00 | 0.01 | 0.00 | 0.02 | 0.14 | 0.00 | 0.01 | 0.05 | 0.03 | 0.05 | 0.00 | 0.00 | 0.02 | 0.31 | 0.01 | 0.09 | 0.01 | 0.08 | 0.02 | 0.03 | 0.04 | 0.05 | 0.03 | 0.06 | 0.01 | 0.05 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.10 | 0.04 | 0.29 | 0.01 | 0.09 | 0.00 | 0.07 | 0.05 | 0.26 | 0.08 | 0.09 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.14 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.00 | 0.02 | 0.15 |
| SLC25A3 | ENSG00000075415 | 0.01 | 0.01 | 0.01 | 0.00 | 0.06 | 0.02 | 0.05 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.06 | 0.02 | 0.04 | 0.02 | 0.03 | 0.03 | 0.05 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.06 | 0.03 | 0.04 | 0.00 | 0.17 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.07 | 0.10 | 0.24 | 0.02 | 0.02 | 0.05 | 0.04 | 0.01 | 0.16 | 0.17 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.08 |
| KCNG3 | ENSG00000171126 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.02 | 0.14 | 0.02 | 0.03 | 0.01 | 0.04 | 0.03 | 0.03 | 0.03 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.25 | 0.05 | 0.08 | 0.00 | 0.07 | 0.02 | 0.18 | 0.00 | 0.05 | 0.06 | 0.17 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 |
| MMP14 | ENSG00000157227 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.12 | 0.07 | 0.01 | 0.00 | 0.00 | 0.02 | 0.16 | 0.02 | 0.13 | 0.07 | 0.07 | 0.07 | 0.09 | 0.07 | 0.06 | 0.04 | 0.03 | 0.02 | 0.01 | 0.07 | 0.01 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.27 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 | 0.29 | 0.12 | 0.08 | 0.02 | 0.06 | 0.03 | 0.08 | 0.07 | 0.16 | 0.05 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
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