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 |
| VEGFB | ENSG00000173511 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.06 | 0.03 | 0.08 | 0.02 | 0.19 | 0.03 | 0.11 | 0.05 | 0.02 | 0.03 | 0.01 | 0.01 | 0.03 | 0.03 | 0.00 | 0.03 | 0.02 | 0.03 | 0.13 | 0.07 | 0.07 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.09 | 0.15 | 0.05 | 0.08 | 0.01 | 0.10 | 0.03 | 0.55 | 0.08 | 0.07 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 |
| PEAK1 | ENSG00000173517 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.04 | 0.00 | 0.00 | 0.09 | 0.01 | 0.04 | 0.01 | 0.09 | 0.02 | 0.02 | 0.05 | 0.07 | 0.04 | 0.06 | 0.05 | 0.02 | 0.02 | 0.03 | 0.04 | 0.04 | 0.01 | 0.04 | 0.03 | 0.05 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.19 | 0.14 | 0.13 | 0.01 | 0.04 | 0.05 | 0.18 | 0.11 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.02 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.19 | 0.01 |
| TNFRSF10D | ENSG00000173530 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.24 | 0.01 | 0.15 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.11 | 0.00 | 0.07 | 0.02 | 0.06 | 0.04 | 0.04 | 0.00 | 0.12 | 0.01 | 0.17 | 0.00 | 0.05 | 0.00 | 0.12 | 0.00 | 0.05 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.18 | 0.00 | 0.45 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.24 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.04 |
| MST1 | ENSG00000173531 | 0.00 | 0.18 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.15 | 0.00 | 0.01 | 0.00 | 0.54 | 0.01 | 0.06 | 0.00 | 0.10 | 0.00 | 0.06 | 0.00 | 0.14 | 0.02 | 0.12 | 0.00 | 0.06 | 0.01 | 0.06 | 0.00 | 0.04 | 0.03 | 0.05 | 0.00 | 0.24 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.09 | 0.20 | 0.00 | 0.07 | 0.06 | 0.06 | 0.00 | 0.30 | 0.04 | 0.16 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.13 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.04 |
| TNFRSF10C | ENSG00000173535 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.24 | 0.01 | 0.15 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.11 | 0.00 | 0.07 | 0.02 | 0.06 | 0.04 | 0.04 | 0.00 | 0.12 | 0.01 | 0.18 | 0.00 | 0.06 | 0.01 | 0.13 | 0.00 | 0.05 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.18 | 0.00 | 0.45 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.24 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 | 0.04 |
| ADGRF3 | ENSG00000173567 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.09 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.06 | 0.01 | 0.09 | 0.01 | 0.03 | 0.01 | 0.07 | 0.04 | 0.04 | 0.03 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.04 | 0.10 | 0.00 | 0.00 | 0.05 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.20 | 0.09 | 0.08 | 0.00 | 0.10 | 0.02 | 0.22 | 0.00 | 0.05 | 0.10 | 0.17 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 |
| XCR1 | ENSG00000173578 | 0.00 | 0.18 | 0.00 | 0.02 | 0.08 | 0.00 | 0.00 | 0.02 | 0.08 | 0.10 | 0.00 | 0.03 | 0.00 | 0.52 | 0.01 | 0.06 | 0.01 | 0.08 | 0.00 | 0.05 | 0.02 | 0.08 | 0.01 | 0.09 | 0.00 | 0.04 | 0.03 | 0.06 | 0.00 | 0.04 | 0.03 | 0.03 | 0.00 | 0.24 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.07 | 0.18 | 0.01 | 0.05 | 0.01 | 0.05 | 0.02 | 0.18 | 0.04 | 0.13 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.02 | 0.05 |
| CCR9 | ENSG00000173585 | 0.00 | 0.18 | 0.00 | 0.02 | 0.08 | 0.00 | 0.00 | 0.02 | 0.08 | 0.10 | 0.00 | 0.03 | 0.00 | 0.50 | 0.01 | 0.06 | 0.00 | 0.08 | 0.00 | 0.05 | 0.02 | 0.08 | 0.01 | 0.09 | 0.00 | 0.04 | 0.03 | 0.06 | 0.00 | 0.04 | 0.04 | 0.03 | 0.00 | 0.24 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.07 | 0.17 | 0.01 | 0.05 | 0.02 | 0.05 | 0.02 | 0.20 | 0.04 | 0.13 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.05 |
| UGT2A1 | ENSG00000173610 | 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 | 0.06 | 0.03 | 0.24 | 0.01 | 0.08 | 0.02 | 0.13 | 0.02 | 0.04 | 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 | 0.03 | 0.00 | 0.00 | 0.09 | 0.02 | 0.25 | 0.09 | 0.04 | 0.03 | 0.04 | 0.01 | 0.06 | 0.05 | 0.07 | 0.06 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| GPRC6A | ENSG00000173612 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.25 | 0.02 | 0.10 | 0.00 | 0.01 | 0.02 | 0.15 | 0.01 | 0.05 | 0.03 | 0.04 | 0.03 | 0.02 | 0.07 | 0.06 | 0.04 | 0.05 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.12 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.07 | 0.07 | 0.26 | 0.01 | 0.02 | 0.05 | 0.02 | 0.07 | 0.05 | 0.20 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.18 | 0.00 | 0.04 | 0.00 | 0.09 | 0.04 | 0.03 | 0.01 | 0.13 |
| SLC19A1 | ENSG00000173638 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.04 | 0.00 | 0.02 | 0.02 | 0.01 | 0.05 | 0.03 | 0.05 | 0.06 | 0.02 | 0.06 | 0.05 | 0.09 | 0.02 | 0.07 | 0.01 | 0.02 | 0.01 | 0.09 | 0.01 | 0.01 | 0.03 | 0.03 | 0.05 | 0.07 | 0.11 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.21 | 0.18 | 0.05 | 0.05 | 0.05 | 0.03 | 0.09 | 0.14 | 0.11 | 0.14 | 0.04 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.02 | 0.04 |
| RCE1 | ENSG00000173653 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.11 | 0.00 | 0.20 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.13 | 0.01 | 0.15 | 0.01 | 0.37 | 0.01 | 0.26 | 0.02 | 0.14 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.11 | 0.01 | 0.01 | 0.02 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.38 | 0.03 | 0.24 | 0.02 | 0.20 | 0.00 | 0.10 | 0.02 | 0.19 | 0.04 | 0.12 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.19 | 0.03 |
| OR1L1 | ENSG00000173679 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.04 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.05 | 0.02 | 0.06 | 0.01 | 0.11 | 0.01 | 0.08 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.06 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.11 | 0.15 | 0.02 | 0.01 | 0.02 | 0.04 | 0.03 | 0.16 | 0.09 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| ADGRG2 | ENSG00000173698 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.11 | 0.04 | 0.02 | 0.02 | 0.08 | 0.05 | 0.03 | 0.02 | 0.00 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.06 | 0.02 | 0.11 | 0.14 | 0.06 | 0.02 | 0.04 | 0.01 | 0.06 | 0.09 | 0.15 | 0.05 | 0.07 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 |
| MUC13 | ENSG00000173702 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.04 | 0.04 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.11 | 0.01 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.27 | 0.04 | 0.08 | 0.01 | 0.06 | 0.01 | 0.09 | 0.08 | 0.10 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 |
| CD7 | ENSG00000173762 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.20 | 0.01 | 0.00 | 0.00 | 0.12 | 0.02 | 0.16 | 0.02 | 0.18 | 0.09 | 0.06 | 0.07 | 0.10 | 0.11 | 0.11 | 0.04 | 0.04 | 0.00 | 0.04 | 0.03 | 0.03 | 0.09 | 0.32 | 0.01 | 0.15 | 0.01 | 0.24 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.34 | 0.05 | 0.43 | 0.08 | 0.08 | 0.10 | 0.17 | 0.02 | 0.51 | 0.08 | 0.21 | 0.17 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.03 | 0.02 | 0.14 | 0.00 | 0.24 | 0.03 |
| KCNH6 | ENSG00000173826 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.26 | 0.00 | 0.02 | 0.00 | 0.12 | 0.00 | 0.13 | 0.01 | 0.18 | 0.01 | 0.07 | 0.02 | 0.25 | 0.02 | 0.13 | 0.02 | 0.09 | 0.01 | 0.08 | 0.03 | 0.08 | 0.11 | 0.19 | 0.00 | 0.12 | 0.01 | 0.17 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.56 | 0.01 | 0.27 | 0.03 | 0.19 | 0.01 | 0.13 | 0.03 | 0.29 | 0.02 | 0.17 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.23 | 0.01 |
| PLK3 | ENSG00000173846 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.09 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.09 | 0.02 | 0.08 | 0.02 | 0.07 | 0.01 | 0.09 | 0.01 | 0.04 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.08 | 0.00 | 0.27 | 0.04 | 0.03 | 0.01 | 0.11 | 0.00 | 0.00 | 0.06 | 0.05 | 0.43 | 0.05 | 0.10 | 0.00 | 0.09 | 0.01 | 0.10 | 0.03 | 0.11 | 0.04 | 0.07 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.03 | 0.02 |
| CBX2 | ENSG00000173894 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.21 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.19 | 0.01 | 0.20 | 0.04 | 0.07 | 0.04 | 0.18 | 0.08 | 0.10 | 0.04 | 0.06 | 0.00 | 0.04 | 0.03 | 0.03 | 0.09 | 0.28 | 0.01 | 0.10 | 0.01 | 0.17 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.39 | 0.03 | 0.45 | 0.04 | 0.12 | 0.08 | 0.18 | 0.01 | 0.63 | 0.04 | 0.19 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.04 | 0.01 | 0.17 | 0.00 | 0.24 | 0.02 |
| SLCO4C1 | ENSG00000173930 | 0.11 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.21 | 0.04 | 0.08 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.06 | 0.00 | 0.08 | 0.00 | 0.07 | 0.04 | 0.10 | 0.02 | 0.13 | 0.00 | 0.14 | 0.02 | 0.05 | 0.00 | 0.05 | 0.03 | 0.03 | 0.00 | 0.02 | 0.09 | 0.02 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.07 | 0.07 | 0.44 | 0.00 | 0.05 | 0.01 | 0.05 | 0.01 | 0.12 | 0.07 | 0.04 | 0.01 | 0.00 | 0.00 | 0.07 | 0.04 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.04 |
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