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 |
| MLX | ENSG00000108788 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.04 | 0.05 | 0.03 | 0.01 | 0.12 | 0.02 | 0.12 | 0.03 | 0.05 | 0.01 | 0.03 | 0.02 | 0.03 | 0.03 | 0.05 | 0.03 | 0.02 | 0.01 | 0.01 | 0.14 | 0.01 | 0.12 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.15 | 0.02 | 0.03 | 0.02 | 0.08 | 0.01 | 0.20 | 0.06 | 0.10 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 |
| CNTNAP1 | ENSG00000108797 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.06 | 0.01 | 0.02 | 0.05 | 0.03 | 0.01 | 0.13 | 0.02 | 0.10 | 0.03 | 0.04 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.05 | 0.03 | 0.02 | 0.01 | 0.01 | 0.14 | 0.01 | 0.12 | 0.00 | 0.00 | 0.04 | 0.10 | 0.01 | 0.15 | 0.02 | 0.03 | 0.02 | 0.08 | 0.01 | 0.19 | 0.04 | 0.10 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 |
| VAT1 | ENSG00000108828 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.06 | 0.01 | 0.03 | 0.05 | 0.02 | 0.01 | 0.12 | 0.01 | 0.09 | 0.03 | 0.04 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.05 | 0.04 | 0.02 | 0.01 | 0.03 | 0.14 | 0.01 | 0.10 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.16 | 0.04 | 0.03 | 0.02 | 0.08 | 0.06 | 0.19 | 0.04 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.03 |
| PPY | ENSG00000108849 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.04 | 0.03 | 0.01 | 0.01 | 0.02 | 0.04 | 0.07 | 0.01 | 0.04 | 0.06 | 0.02 | 0.02 | 0.11 | 0.01 | 0.10 | 0.02 | 0.02 | 0.01 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.03 | 0.08 | 0.01 | 0.07 | 0.14 | 0.00 | 0.09 | 0.00 | 0.00 | 0.03 | 0.10 | 0.03 | 0.14 | 0.04 | 0.03 | 0.04 | 0.06 | 0.08 | 0.19 | 0.05 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.05 |
| EFNB3 | ENSG00000108947 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.25 | 0.02 | 0.07 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.03 | 0.01 | 0.04 | 0.03 | 0.04 | 0.01 | 0.04 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.16 | 0.01 | 0.12 | 0.02 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.07 | 0.11 | 0.04 | 0.00 | 0.04 | 0.04 | 0.04 | 0.09 | 0.16 | 0.09 | 0.61 | 0.00 | 0.02 | 0.02 | 0.02 | 0.00 | 0.10 | 0.00 | 0.01 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.05 |
| FAM20A | ENSG00000108950 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.22 | 0.01 | 0.05 | 0.00 | 0.12 | 0.00 | 0.16 | 0.00 | 0.20 | 0.01 | 0.07 | 0.02 | 0.23 | 0.03 | 0.14 | 0.04 | 0.08 | 0.01 | 0.09 | 0.02 | 0.05 | 0.10 | 0.21 | 0.02 | 0.12 | 0.01 | 0.15 | 0.18 | 0.02 | 0.01 | 0.00 | 0.00 | 0.50 | 0.02 | 0.27 | 0.03 | 0.15 | 0.03 | 0.13 | 0.01 | 0.29 | 0.02 | 0.22 | 0.03 | 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 |
| DHRS7B | ENSG00000109016 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.17 | 0.07 | 0.04 | 0.01 | 0.01 | 0.02 | 0.07 | 0.04 | 0.10 | 0.06 | 0.03 | 0.05 | 0.03 | 0.10 | 0.02 | 0.07 | 0.06 | 0.03 | 0.03 | 0.08 | 0.01 | 0.01 | 0.07 | 0.04 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.14 | 0.04 | 0.05 | 0.14 | 0.07 | 0.05 | 0.08 | 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 |
| GABRA4 | ENSG00000109158 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.04 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.09 | 0.02 | 0.12 | 0.03 | 0.03 | 0.02 | 0.10 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.02 | 0.02 | 0.04 | 0.00 | 0.00 | 0.07 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.14 | 0.03 | 0.01 | 0.02 | 0.02 | 0.01 | 0.10 | 0.00 | 0.07 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.05 | 0.00 | 0.03 | 0.01 |
| GNRHR | ENSG00000109163 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.04 | 0.02 | 0.18 | 0.02 | 0.07 | 0.01 | 0.12 | 0.01 | 0.03 | 0.03 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.03 | 0.03 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.20 | 0.09 | 0.04 | 0.04 | 0.04 | 0.02 | 0.02 | 0.05 | 0.10 | 0.06 | 0.10 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 |
| UGT2B10 | ENSG00000109181 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.11 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.03 | 0.21 | 0.01 | 0.08 | 0.02 | 0.13 | 0.01 | 0.03 | 0.02 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.01 | 0.06 | 0.00 | 0.03 | 0.03 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.20 | 0.08 | 0.04 | 0.04 | 0.04 | 0.01 | 0.02 | 0.05 | 0.06 | 0.06 | 0.09 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 |
| SULT1E1 | ENSG00000109193 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.12 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.03 | 0.23 | 0.01 | 0.08 | 0.02 | 0.14 | 0.02 | 0.05 | 0.03 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.04 | 0.07 | 0.00 | 0.03 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.26 | 0.08 | 0.04 | 0.04 | 0.04 | 0.01 | 0.06 | 0.05 | 0.05 | 0.05 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| ODAM | ENSG00000109205 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.03 | 0.21 | 0.01 | 0.08 | 0.02 | 0.10 | 0.02 | 0.05 | 0.03 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.03 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 | 0.24 | 0.08 | 0.04 | 0.04 | 0.04 | 0.02 | 0.06 | 0.05 | 0.07 | 0.05 | 0.09 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| SMR3A | ENSG00000109208 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.03 | 0.21 | 0.01 | 0.08 | 0.02 | 0.10 | 0.02 | 0.05 | 0.03 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.08 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 | 0.24 | 0.08 | 0.04 | 0.04 | 0.04 | 0.01 | 0.10 | 0.05 | 0.07 | 0.06 | 0.10 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| NMU | ENSG00000109255 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.11 | 0.02 | 0.51 | 0.01 | 0.09 | 0.00 | 0.14 | 0.05 | 0.04 | 0.03 | 0.03 | 0.01 | 0.04 | 0.04 | 0.04 | 0.02 | 0.03 | 0.04 | 0.00 | 0.08 | 0.03 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.01 | 0.20 | 0.04 | 0.12 | 0.01 | 0.04 | 0.00 | 0.10 | 0.02 | 0.22 | 0.03 | 0.33 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.13 | 0.01 | 0.32 | 0.01 | 0.03 | 0.00 | 0.10 | 0.01 |
| PF4V1 | ENSG00000109272 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.07 | 0.02 | 0.23 | 0.01 | 0.10 | 0.01 | 0.20 | 0.02 | 0.07 | 0.02 | 0.02 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.08 | 0.00 | 0.03 | 0.07 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.31 | 0.11 | 0.07 | 0.03 | 0.03 | 0.01 | 0.05 | 0.05 | 0.07 | 0.06 | 0.09 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| AREG | ENSG00000109321 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.07 | 0.02 | 0.20 | 0.02 | 0.09 | 0.01 | 0.21 | 0.02 | 0.08 | 0.02 | 0.02 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.08 | 0.00 | 0.03 | 0.11 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.14 | 0.02 | 0.29 | 0.11 | 0.05 | 0.02 | 0.03 | 0.01 | 0.05 | 0.05 | 0.08 | 0.06 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| UCP1 | ENSG00000109424 | 0.01 | 0.01 | 0.00 | 0.01 | 0.06 | 0.00 | 0.02 | 0.01 | 0.06 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.04 | 0.02 | 0.09 | 0.03 | 0.04 | 0.08 | 0.03 | 0.07 | 0.04 | 0.01 | 0.02 | 0.02 | 0.02 | 0.00 | 0.02 | 0.04 | 0.05 | 0.00 | 0.03 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.16 | 0.03 | 0.05 | 0.04 | 0.03 | 0.11 | 0.04 | 0.09 | 0.08 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.07 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.03 |
| IL2 | ENSG00000109471 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.07 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.04 | 0.03 | 0.06 | 0.02 | 0.02 | 0.01 | 0.05 | 0.02 | 0.06 | 0.01 | 0.04 | 0.02 | 0.02 | 0.00 | 0.02 | 0.04 | 0.05 | 0.00 | 0.11 | 0.11 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.05 | 0.24 | 0.01 | 0.04 | 0.01 | 0.03 | 0.04 | 0.07 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 |
| SOD3 | ENSG00000109610 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.01 | 0.06 | 0.04 | 0.05 | 0.05 | 0.04 | 0.02 | 0.02 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.10 | 0.07 | 0.00 | 0.02 | 0.03 | 0.04 | 0.08 | 0.07 | 0.12 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.04 | 0.01 |
| CPZ | ENSG00000109625 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.04 | 0.04 | 0.03 | 0.06 | 0.09 | 0.09 | 0.05 | 0.04 | 0.02 | 0.03 | 0.03 | 0.03 | 0.02 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.04 | 0.23 | 0.06 | 0.01 | 0.03 | 0.05 | 0.03 | 0.13 | 0.00 | 0.06 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.05 | 0.03 |
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