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 |
| P2RY2 | ENSG00000175591 | 0.00 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.04 | 0.00 | 0.19 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.14 | 0.01 | 0.22 | 0.02 | 0.33 | 0.02 | 0.59 | 0.03 | 0.14 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.07 | 0.02 | 0.08 | 0.02 | 0.06 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.37 | 0.06 | 0.51 | 0.04 | 0.13 | 0.01 | 0.11 | 0.02 | 0.19 | 0.08 | 0.16 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.27 | 0.01 |
| ABCA12 | ENSG00000144452 | 0.01 | 0.06 | 0.04 | 0.03 | 0.00 | 0.03 | 0.01 | 0.03 | 0.02 | 0.26 | 0.00 | 0.00 | 0.00 | 0.15 | 0.03 | 0.03 | 0.03 | 0.19 | 0.01 | 0.18 | 0.03 | 0.11 | 0.05 | 0.06 | 0.02 | 0.02 | 0.02 | 0.03 | 0.06 | 0.03 | 0.03 | 0.05 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.05 | 0.18 | 0.16 | 0.03 | 0.33 | 0.03 | 0.05 | 0.08 | 0.05 | 0.05 | 0.18 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.04 |
| CHEK2 | ENSG00000183765 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.15 | 0.04 | 0.00 | 0.07 | 0.01 | 0.08 | 0.03 | 0.03 | 0.15 | 0.01 | 0.05 | 0.01 | 0.04 | 0.02 | 0.03 | 0.03 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.11 | 0.01 | 0.15 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.15 | 0.09 | 0.03 | 0.01 | 0.06 | 0.04 | 0.26 | 0.03 | 0.04 | 0.05 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.07 |
| FGL1 | ENSG00000104760 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.19 | 0.00 | 0.14 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.07 | 0.01 | 0.09 | 0.00 | 0.07 | 0.05 | 0.05 | 0.12 | 0.03 | 0.00 | 0.11 | 0.00 | 0.18 | 0.00 | 0.05 | 0.01 | 0.13 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.14 | 0.03 | 0.38 | 0.00 | 0.04 | 0.01 | 0.08 | 0.16 | 0.18 | 0.06 | 0.03 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.02 | 0.04 |
| SLC7A8 | ENSG00000092068 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.03 | 0.16 | 0.07 | 0.07 | 0.07 | 0.12 | 0.06 | 0.06 | 0.04 | 0.02 | 0.02 | 0.01 | 0.07 | 0.01 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.33 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 | 0.28 | 0.12 | 0.08 | 0.03 | 0.06 | 0.03 | 0.10 | 0.07 | 0.23 | 0.03 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| IL13RA1 | ENSG00000131724 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.03 | 0.03 | 0.00 | 0.03 | 0.01 | 0.09 | 0.01 | 0.11 | 0.01 | 0.05 | 0.01 | 0.10 | 0.02 | 0.09 | 0.03 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.07 | 0.02 | 0.03 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.16 | 0.03 | 0.06 | 0.01 | 0.02 | 0.01 | 0.01 | 0.05 | 0.04 | 0.12 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| PGR | ENSG00000082175 | 0.01 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.02 | 0.05 | 0.21 | 0.06 | 0.00 | 0.00 | 0.06 | 0.06 | 0.10 | 0.04 | 0.07 | 0.08 | 0.33 | 0.09 | 0.17 | 0.06 | 0.07 | 0.04 | 0.02 | 0.03 | 0.02 | 0.04 | 0.01 | 0.01 | 0.04 | 0.06 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.07 | 0.16 | 0.31 | 0.12 | 0.62 | 0.09 | 0.06 | 0.04 | 0.10 | 0.16 | 0.11 | 0.13 | 0.02 | 0.07 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.19 | 0.11 |
| KCNH2 | ENSG00000055118 | 0.03 | 0.01 | 0.04 | 0.00 | 0.09 | 0.02 | 0.03 | 0.03 | 0.05 | 0.05 | 0.00 | 0.01 | 0.00 | 0.03 | 0.10 | 0.02 | 0.09 | 0.09 | 0.02 | 0.17 | 0.07 | 0.26 | 0.02 | 0.10 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.07 | 0.53 | 0.08 | 0.04 | 0.09 | 0.04 | 0.06 | 0.07 | 0.19 | 0.11 | 0.15 | 0.01 | 0.05 | 0.00 | 0.06 | 0.02 | 0.09 | 0.10 | 0.01 | 0.07 | 0.01 | 0.00 | 0.03 | 0.20 | 0.03 |
| KDM3A | ENSG00000115548 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.11 | 0.01 | 0.06 | 0.01 | 0.14 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 | 0.12 | 0.04 | 0.05 | 0.01 | 0.03 | 0.02 | 0.09 | 0.03 | 0.23 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 |
| FUT2 | ENSG00000176920 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.08 | 0.04 | 0.10 | 0.02 | 0.02 | 0.07 | 0.05 | 0.06 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.04 | 0.04 | 0.00 | 0.07 | 0.21 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.04 | 0.34 | 0.05 | 0.07 | 0.03 | 0.06 | 0.18 | 0.22 | 0.02 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.00 | 0.13 | 0.01 | 0.13 | 0.00 | 0.00 | 0.02 | 0.03 |
| TNK2 | ENSG00000061938 | 0.05 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.06 | 0.19 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.14 | 0.06 | 1.38 | 0.01 | 0.57 | 0.00 | 0.82 | 0.04 | 0.23 | 0.02 | 0.06 | 0.01 | 0.06 | 0.02 | 0.03 | 0.01 | 0.12 | 0.03 | 0.12 | 0.03 | 0.10 | 0.03 | 0.00 | 0.10 | 0.00 | 0.00 | 0.22 | 0.03 | 1.02 | 0.09 | 0.65 | 0.00 | 0.37 | 0.01 | 0.79 | 0.15 | 0.09 | 0.14 | 0.14 | 0.03 | 0.01 | 0.00 | 0.35 | 0.04 | 0.03 | 0.07 | 0.06 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| KLHL8 | ENSG00000145332 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.13 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.07 | 0.04 | 0.05 | 0.02 | 0.04 | 0.07 | 0.03 | 0.07 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.11 | 0.00 | 0.03 | 0.09 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.04 | 0.05 | 0.22 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.09 | 0.05 | 0.08 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 |
| CACNG2 | ENSG00000166862 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.15 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.06 | 0.04 | 0.06 | 0.02 | 0.01 | 0.01 | 0.03 | 0.03 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 | 0.08 | 0.11 | 0.03 | 0.01 | 0.05 | 0.02 | 0.42 | 0.06 | 0.08 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.10 | 0.02 |
| LAMA1 | ENSG00000101680 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.06 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.04 | 0.01 | 0.07 | 0.01 | 0.11 | 0.10 | 0.05 | 0.02 | 0.01 | 0.04 | 0.01 | 0.03 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.10 | 0.08 | 0.05 | 0.02 | 0.03 | 0.01 | 0.06 | 0.02 | 0.14 | 0.04 | 0.02 | 0.06 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 |
| WNT7A | ENSG00000154764 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.41 | 0.01 | 0.00 | 0.03 | 0.03 | 0.03 | 0.04 | 0.05 | 0.02 | 0.04 | 0.02 | 0.02 | 0.04 | 0.05 | 0.06 | 0.05 | 0.01 | 0.03 | 0.03 | 0.06 | 0.01 | 0.01 | 0.06 | 0.01 | 0.00 | 0.18 | 0.07 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.03 | 0.15 | 0.21 | 0.04 | 0.01 | 0.18 | 0.04 | 0.63 | 0.11 | 0.24 | 0.01 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 |
| ADRBK1 | ENSG00000173020 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.11 | 0.00 | 0.23 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.14 | 0.01 | 0.17 | 0.01 | 0.44 | 0.00 | 0.41 | 0.02 | 0.19 | 0.02 | 0.01 | 0.01 | 0.04 | 0.02 | 0.02 | 0.01 | 0.14 | 0.01 | 0.20 | 0.02 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.49 | 0.03 | 0.27 | 0.02 | 0.21 | 0.00 | 0.16 | 0.02 | 0.27 | 0.02 | 0.13 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.18 | 0.02 |
| SLC6A2 | ENSG00000103546 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.03 | 0.04 | 0.02 | 0.03 | 0.03 | 0.10 | 0.01 | 0.02 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.06 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.04 | 0.04 | 0.15 | 0.01 | 0.08 | 0.03 | 0.06 | 0.05 | 0.12 | 0.02 | 0.08 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.00 | 0.05 |
| MAPT | ENSG00000186868 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.03 | 0.01 | 0.00 | 0.03 | 0.00 | 0.05 | 0.02 | 0.09 | 0.03 | 0.01 | 0.01 | 0.08 | 0.03 | 0.11 | 0.02 | 0.02 | 0.01 | 0.03 | 0.03 | 0.03 | 0.02 | 0.01 | 0.03 | 0.02 | 0.01 | 0.01 | 0.08 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.11 | 0.03 | 0.12 | 0.03 | 0.02 | 0.02 | 0.06 | 0.05 | 0.19 | 0.05 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.05 |
| DPEP1 | ENSG00000015413 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.06 | 0.01 | 0.23 | 0.08 | 0.06 | 0.00 | 0.00 | 0.02 | 0.19 | 0.01 | 0.12 | 0.04 | 0.07 | 0.03 | 0.05 | 0.08 | 0.05 | 0.05 | 0.05 | 0.02 | 0.03 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.08 | 0.05 | 0.05 | 0.07 | 0.06 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.10 | 0.08 | 0.35 | 0.05 | 0.07 | 0.01 | 0.09 | 0.03 | 0.29 | 0.09 | 0.07 | 0.00 | 0.12 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.06 | 0.02 | 0.11 |
| TMPRSS6 | ENSG00000187045 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.11 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.06 | 0.04 | 0.06 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 | 0.08 | 0.11 | 0.03 | 0.01 | 0.05 | 0.02 | 0.28 | 0.06 | 0.04 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.02 |
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