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 |
| PARP9 | ENSG00000138496 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.05 | 0.02 | 0.11 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.25 | 0.04 | 0.06 | 0.01 | 0.04 | 0.01 | 0.05 | 0.09 | 0.08 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 |
| SPPL2A | ENSG00000138600 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.00 | 0.01 | 0.04 | 0.06 | 0.03 | 0.00 | 0.00 | 0.07 | 0.11 | 0.01 | 0.04 | 0.04 | 0.06 | 0.03 | 0.03 | 0.03 | 0.02 | 0.02 | 0.06 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.06 | 0.19 | 0.01 | 0.09 | 0.01 | 0.07 | 0.08 | 0.26 | 0.09 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.00 | 0.02 | 0.01 | 0.08 | 0.00 | 0.00 | 0.04 | 0.10 |
| APH1B | ENSG00000138613 | 0.00 | 0.00 | 0.00 | 0.01 | 0.19 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.04 | 0.03 | 0.05 | 0.02 | 0.02 | 0.02 | 0.03 | 0.03 | 0.04 | 0.04 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.11 | 0.11 | 0.05 | 0.01 | 0.04 | 0.05 | 0.07 | 0.19 | 0.12 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 |
| HCN4 | ENSG00000138622 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.09 | 0.00 | 0.04 | 0.02 | 0.06 | 0.01 | 0.03 | 0.02 | 0.07 | 0.02 | 0.06 | 0.03 | 0.02 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.03 | 0.03 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.18 | 0.11 | 0.10 | 0.01 | 0.02 | 0.04 | 0.14 | 0.03 | 0.05 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.00 |
| FGF5 | ENSG00000138675 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.08 | 0.04 | 0.00 | 0.00 | 0.02 | 0.07 | 0.04 | 0.03 | 0.10 | 0.04 | 0.04 | 0.03 | 0.04 | 0.06 | 0.02 | 0.06 | 0.01 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.03 | 0.10 | 0.05 | 0.03 | 0.06 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.09 | 0.19 | 0.03 | 0.03 | 0.02 | 0.02 | 0.03 | 0.09 | 0.07 | 0.05 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 |
| IL21 | ENSG00000138684 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.08 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.04 | 0.03 | 0.06 | 0.03 | 0.02 | 0.01 | 0.05 | 0.02 | 0.06 | 0.01 | 0.04 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.05 | 0.00 | 0.11 | 0.11 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 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 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| TRPC3 | ENSG00000138741 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.03 | 0.06 | 0.02 | 0.02 | 0.01 | 0.04 | 0.02 | 0.06 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.02 | 0.03 | 0.07 | 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 | 0.04 | 0.04 | 0.07 | 0.07 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| NAAA | ENSG00000138744 | 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 | 0.03 | 0.23 | 0.01 | 0.08 | 0.01 | 0.20 | 0.03 | 0.07 | 0.04 | 0.01 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.02 | 0.08 | 0.05 | 0.03 | 0.04 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.14 | 0.02 | 0.23 | 0.12 | 0.07 | 0.02 | 0.03 | 0.01 | 0.05 | 0.05 | 0.08 | 0.06 | 0.06 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| CXCL9 | ENSG00000138755 | 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 | 0.21 | 0.01 | 0.08 | 0.01 | 0.20 | 0.03 | 0.07 | 0.05 | 0.01 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.02 | 0.08 | 0.05 | 0.03 | 0.04 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.13 | 0.02 | 0.22 | 0.12 | 0.07 | 0.02 | 0.03 | 0.01 | 0.05 | 0.05 | 0.08 | 0.06 | 0.06 | 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 |
| CNOT6L | ENSG00000138767 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.08 | 0.06 | 0.02 | 0.15 | 0.03 | 0.05 | 0.03 | 0.07 | 0.04 | 0.06 | 0.03 | 0.01 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.09 | 0.00 | 0.08 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.10 | 0.03 | 0.11 | 0.19 | 0.06 | 0.03 | 0.03 | 0.01 | 0.05 | 0.05 | 0.06 | 0.07 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| ENPEP | ENSG00000138792 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.05 | 0.01 | 0.01 | 0.05 | 0.04 | 0.02 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 | 0.09 | 0.00 | 0.11 | 0.09 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.04 | 0.05 | 0.04 | 0.26 | 0.01 | 0.02 | 0.02 | 0.05 | 0.04 | 0.11 | 0.07 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.06 |
| CASP6 | ENSG00000138794 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.03 | 0.03 | 0.05 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.09 | 0.00 | 0.11 | 0.12 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.06 | 0.04 | 0.28 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.11 | 0.08 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 |
| SLC39A8 | ENSG00000138821 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.03 | 0.07 | 0.02 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.12 | 0.00 | 0.03 | 0.10 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.05 | 0.05 | 0.03 | 0.31 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.11 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.05 |
| MTTP | ENSG00000138823 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.03 | 0.04 | 0.05 | 0.01 | 0.02 | 0.02 | 0.08 | 0.02 | 0.04 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.11 | 0.00 | 0.03 | 0.04 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.02 | 0.29 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.11 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 |
| PDE6H | ENSG00000139053 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.10 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.06 | 0.05 | 0.09 | 0.09 | 0.02 | 0.05 | 0.03 | 0.13 | 0.03 | 0.04 | 0.07 | 0.01 | 0.03 | 0.00 | 0.06 | 0.03 | 0.05 | 0.00 | 0.04 | 0.14 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.06 | 0.24 | 0.12 | 0.01 | 0.03 | 0.03 | 0.02 | 0.15 | 0.03 | 0.11 | 0.13 | 0.56 | 0.00 | 0.00 | 0.05 | 0.00 | 0.04 | 0.04 | 0.02 | 0.00 | 0.06 | 0.00 | 0.01 | 0.04 | 0.03 |
| YARS2 | ENSG00000139131 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.09 | 0.02 | 0.00 | 0.00 | 0.04 | 0.01 | 0.16 | 0.04 | 0.15 | 0.01 | 0.06 | 0.01 | 0.14 | 0.02 | 0.07 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.07 | 0.02 | 0.02 | 0.02 | 0.00 | 0.05 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.35 | 0.02 | 0.02 | 0.01 | 0.06 | 0.01 | 0.10 | 0.03 | 0.14 | 0.05 | 0.41 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 |
| METTL20 | ENSG00000139160 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.13 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.16 | 0.03 | 0.19 | 0.01 | 0.08 | 0.01 | 0.19 | 0.02 | 0.12 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.11 | 0.02 | 0.02 | 0.02 | 0.00 | 0.05 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.41 | 0.02 | 0.02 | 0.02 | 0.07 | 0.01 | 0.17 | 0.06 | 0.15 | 0.05 | 0.42 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.06 | 0.01 |
| C1RL | ENSG00000139178 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.06 | 0.07 | 0.16 | 0.01 | 0.11 | 0.02 | 0.07 | 0.02 | 0.05 | 0.05 | 0.05 | 0.02 | 0.04 | 0.03 | 0.06 | 0.06 | 0.06 | 0.05 | 0.18 | 0.05 | 0.08 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.12 | 0.04 | 0.32 | 0.08 | 0.04 | 0.02 | 0.08 | 0.02 | 0.11 | 0.03 | 0.09 | 0.11 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.14 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 |
| VAMP1 | ENSG00000139190 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.06 | 0.07 | 0.17 | 0.01 | 0.11 | 0.01 | 0.08 | 0.05 | 0.06 | 0.05 | 0.06 | 0.02 | 0.05 | 0.02 | 0.05 | 0.05 | 0.04 | 0.04 | 0.14 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.37 | 0.08 | 0.05 | 0.02 | 0.09 | 0.02 | 0.12 | 0.03 | 0.11 | 0.12 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.05 | 0.04 |
| TAPBPL | ENSG00000139192 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.07 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.08 | 0.06 | 0.07 | 0.17 | 0.01 | 0.11 | 0.01 | 0.08 | 0.05 | 0.06 | 0.05 | 0.06 | 0.02 | 0.05 | 0.02 | 0.05 | 0.05 | 0.04 | 0.04 | 0.14 | 0.05 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.38 | 0.08 | 0.05 | 0.02 | 0.09 | 0.02 | 0.12 | 0.03 | 0.11 | 0.12 | 0.60 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.05 | 0.04 |
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