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 |
| PDE1B | ENSG00000123360 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.01 | 0.04 | 0.02 | 0.02 | 0.02 | 0.05 | 0.03 | 0.07 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.30 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.19 | 0.05 | 0.06 | 0.00 | 0.05 | 0.01 | 0.14 | 0.09 | 0.16 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.04 | 0.08 | 0.05 | 0.08 | 0.00 | 0.03 | 0.05 |
| TUBA1B | ENSG00000123416 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.01 | 0.02 | 0.02 | 0.01 | 0.04 | 0.06 | 0.05 | 0.04 | 0.03 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.01 | 0.01 | 0.09 | 0.01 | 0.17 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.05 | 0.08 | 0.07 | 0.02 | 0.01 | 0.04 | 0.01 | 0.09 | 0.11 | 0.07 | 0.09 | 0.02 | 0.00 | 0.00 | 0.01 | 0.10 | 0.06 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.00 | 0.05 | 0.04 |
| DBH | ENSG00000123454 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.07 | 0.03 | 0.06 | 0.03 | 0.12 | 0.04 | 0.12 | 0.01 | 0.02 | 0.01 | 0.05 | 0.03 | 0.01 | 0.00 | 0.05 | 0.03 | 0.06 | 0.01 | 0.12 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.06 | 0.07 | 0.24 | 0.07 | 0.01 | 0.01 | 0.06 | 0.03 | 0.14 | 0.05 | 0.14 | 0.03 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 |
| IL13RA2 | ENSG00000123496 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.03 | 0.03 | 0.00 | 0.00 | 0.06 | 0.06 | 0.01 | 0.10 | 0.01 | 0.04 | 0.01 | 0.09 | 0.02 | 0.05 | 0.04 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.09 | 0.06 | 0.06 | 0.01 | 0.03 | 0.01 | 0.01 | 0.02 | 0.06 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SERPINA7 | ENSG00000123561 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.03 | 0.03 | 0.00 | 0.00 | 0.04 | 0.03 | 0.02 | 0.12 | 0.01 | 0.04 | 0.01 | 0.10 | 0.02 | 0.08 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.05 | 0.03 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.07 | 0.10 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 |
| NRK | ENSG00000123572 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.03 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 | 0.02 | 0.13 | 0.01 | 0.04 | 0.01 | 0.10 | 0.02 | 0.06 | 0.02 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.02 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.08 | 0.05 | 0.04 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.10 | 0.10 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 |
| ATXN3L | ENSG00000123594 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.09 | 0.05 | 0.02 | 0.02 | 0.07 | 0.03 | 0.07 | 0.03 | 0.01 | 0.01 | 0.10 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.13 | 0.17 | 0.06 | 0.00 | 0.04 | 0.02 | 0.10 | 0.12 | 0.14 | 0.06 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 |
| RAB9A | ENSG00000123595 | 0.00 | 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 | 0.03 | 0.05 | 0.08 | 0.05 | 0.02 | 0.02 | 0.07 | 0.03 | 0.05 | 0.02 | 0.01 | 0.01 | 0.13 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.15 | 0.18 | 0.06 | 0.00 | 0.04 | 0.02 | 0.06 | 0.10 | 0.09 | 0.06 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 |
| ACVR1C | ENSG00000123612 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.07 | 0.04 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.01 | 0.09 | 0.02 | 0.05 | 0.01 | 0.09 | 0.03 | 0.05 | 0.04 | 0.00 | 0.01 | 0.00 | 0.01 | 0.05 | 0.01 | 0.05 | 0.06 | 0.00 | 0.05 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.28 | 0.05 | 0.04 | 0.01 | 0.04 | 0.01 | 0.01 | 0.00 | 0.07 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 |
| PLA2G12A | ENSG00000123739 | 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 | 0.03 | 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 | 0.05 | 0.04 | 0.27 | 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 |
| GPR83 | ENSG00000123901 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.03 | 0.03 | 0.12 | 0.05 | 0.00 | 0.00 | 0.06 | 0.06 | 0.07 | 0.04 | 0.06 | 0.09 | 0.09 | 0.10 | 0.10 | 0.05 | 0.08 | 0.04 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.05 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.09 | 0.12 | 0.31 | 0.09 | 0.13 | 0.07 | 0.05 | 0.03 | 0.06 | 0.16 | 0.04 | 0.13 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.10 |
| MC3R | ENSG00000124089 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.06 | 0.04 | 0.00 | 0.00 | 0.03 | 0.00 | 0.17 | 0.02 | 0.04 | 0.03 | 0.01 | 0.01 | 0.11 | 0.01 | 0.17 | 0.00 | 0.13 | 0.00 | 0.13 | 0.00 | 0.02 | 0.01 | 0.10 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.33 | 0.02 | 0.35 | 0.04 | 0.03 | 0.02 | 0.08 | 0.01 | 0.16 | 0.00 | 0.18 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.00 |
| PI3 | ENSG00000124102 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.08 | 0.01 | 0.01 | 0.02 | 0.12 | 0.00 | 0.21 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.02 | 0.24 | 0.05 | 0.03 | 0.05 | 0.11 | 0.01 | 0.39 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| SLPI | ENSG00000124107 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.20 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.09 | 0.01 | 0.01 | 0.02 | 0.11 | 0.00 | 0.21 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.26 | 0.05 | 0.03 | 0.05 | 0.12 | 0.01 | 0.37 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 |
| KCNS1 | ENSG00000124134 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.07 | 0.01 | 0.02 | 0.02 | 0.13 | 0.00 | 0.20 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.02 | 0.24 | 0.05 | 0.03 | 0.05 | 0.11 | 0.01 | 0.39 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 |
| SDC4 | ENSG00000124145 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.09 | 0.01 | 0.01 | 0.02 | 0.10 | 0.00 | 0.21 | 0.00 | 0.19 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.25 | 0.05 | 0.03 | 0.05 | 0.11 | 0.01 | 0.35 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 |
| PIGT | ENSG00000124155 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.09 | 0.01 | 0.01 | 0.01 | 0.09 | 0.00 | 0.21 | 0.00 | 0.19 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.23 | 0.05 | 0.02 | 0.04 | 0.12 | 0.01 | 0.29 | 0.00 | 0.11 | 0.04 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 |
| SEMG2 | ENSG00000124157 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.09 | 0.01 | 0.01 | 0.02 | 0.12 | 0.00 | 0.21 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.25 | 0.05 | 0.03 | 0.05 | 0.10 | 0.01 | 0.45 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 |
| MATN4 | ENSG00000124159 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.21 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.09 | 0.01 | 0.01 | 0.02 | 0.11 | 0.00 | 0.21 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 | 0.26 | 0.05 | 0.03 | 0.05 | 0.11 | 0.01 | 0.35 | 0.00 | 0.11 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 |
| EDN3 | ENSG00000124205 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.03 | 0.00 | 0.25 | 0.01 | 0.04 | 0.03 | 0.01 | 0.01 | 0.11 | 0.01 | 0.17 | 0.00 | 0.13 | 0.00 | 0.07 | 0.00 | 0.05 | 0.00 | 0.07 | 0.01 | 0.00 | 0.01 | 0.05 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.36 | 0.02 | 0.37 | 0.05 | 0.03 | 0.03 | 0.10 | 0.01 | 0.17 | 0.00 | 0.23 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.11 | 0.01 |
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