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 |
| HCN3 | ENSG00000143630 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.08 | 0.01 | 0.36 | 0.02 | 0.02 | 0.00 | 0.11 | 0.00 | 0.37 | 0.00 | 0.27 | 0.00 | 0.05 | 0.01 | 0.20 | 0.00 | 0.16 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.09 | 0.00 | 0.37 | 0.00 | 0.65 | 0.01 | 0.18 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.33 | 0.00 | 0.58 | 0.02 | 0.19 | 0.00 | 0.24 | 0.00 | 1.03 | 0.01 | 0.36 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.02 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.19 | 0.00 |
| MLK4 | ENSG00000143674 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.12 | 0.04 | 0.02 | 0.00 | 0.05 | 0.03 | 0.09 | 0.01 | 0.11 | 0.02 | 0.06 | 0.00 | 0.20 | 0.03 | 0.10 | 0.02 | 0.03 | 0.03 | 0.04 | 0.07 | 0.01 | 0.01 | 0.17 | 0.01 | 0.23 | 0.02 | 0.04 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.25 | 0.02 | 0.44 | 0.08 | 0.08 | 0.02 | 0.09 | 0.02 | 0.28 | 0.00 | 0.02 | 0.23 | 0.04 | 0.04 | 0.02 | 0.00 | 0.02 | 0.15 | 0.00 | 0.03 | 0.02 | 0.04 | 0.09 | 0.03 | 0.15 | 0.03 |
| ACP1 | ENSG00000143727 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.08 | 0.02 | 0.01 | 0.16 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.05 | 0.03 | 0.12 | 0.05 | 0.03 | 0.04 | 0.06 | 0.07 | 0.03 | 0.04 | 0.02 | 0.02 | 0.04 | 0.04 | 0.01 | 0.04 | 0.11 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.33 | 0.18 | 0.09 | 0.02 | 0.12 | 0.04 | 0.30 | 0.07 | 0.03 | 0.21 | 0.14 | 0.02 | 0.00 | 0.00 | 0.02 | 0.08 | 0.03 | 0.03 | 0.02 | 0.04 | 0.05 | 0.00 | 0.04 | 0.04 |
| LEFTY2 | ENSG00000143768 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.09 | 0.04 | 0.02 | 0.02 | 0.05 | 0.01 | 0.09 | 0.01 | 0.13 | 0.01 | 0.05 | 0.00 | 0.25 | 0.05 | 0.13 | 0.01 | 0.03 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.14 | 0.03 | 0.18 | 0.02 | 0.04 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.23 | 0.02 | 0.40 | 0.05 | 0.08 | 0.01 | 0.10 | 0.02 | 0.26 | 0.00 | 0.04 | 0.24 | 0.03 | 0.05 | 0.02 | 0.00 | 0.03 | 0.15 | 0.01 | 0.02 | 0.02 | 0.05 | 0.09 | 0.00 | 0.13 | 0.05 |
| PSEN2 | ENSG00000143801 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.10 | 0.04 | 0.02 | 0.02 | 0.05 | 0.01 | 0.08 | 0.01 | 0.13 | 0.01 | 0.05 | 0.00 | 0.19 | 0.04 | 0.09 | 0.01 | 0.03 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.14 | 0.03 | 0.18 | 0.02 | 0.04 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.23 | 0.02 | 0.40 | 0.05 | 0.07 | 0.01 | 0.08 | 0.02 | 0.23 | 0.00 | 0.03 | 0.25 | 0.03 | 0.05 | 0.02 | 0.00 | 0.02 | 0.18 | 0.02 | 0.02 | 0.03 | 0.05 | 0.09 | 0.03 | 0.11 | 0.05 |
| WNT9A | ENSG00000143816 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.11 | 0.05 | 0.02 | 0.02 | 0.05 | 0.03 | 0.09 | 0.01 | 0.12 | 0.01 | 0.05 | 0.00 | 0.19 | 0.04 | 0.09 | 0.01 | 0.03 | 0.01 | 0.05 | 0.01 | 0.01 | 0.01 | 0.13 | 0.02 | 0.23 | 0.02 | 0.04 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.23 | 0.02 | 0.40 | 0.05 | 0.07 | 0.01 | 0.09 | 0.02 | 0.26 | 0.00 | 0.03 | 0.22 | 0.03 | 0.05 | 0.02 | 0.00 | 0.02 | 0.18 | 0.01 | 0.02 | 0.02 | 0.05 | 0.09 | 0.03 | 0.12 | 0.05 |
| REN | ENSG00000143839 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.12 | 0.00 | 0.15 | 0.00 | 0.13 | 0.01 | 0.05 | 0.00 | 0.15 | 0.06 | 0.06 | 0.01 | 0.04 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.05 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.27 | 0.00 | 0.32 | 0.06 | 0.06 | 0.00 | 0.13 | 0.01 | 0.22 | 0.00 | 0.16 | 0.13 | 0.05 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.17 | 0.01 | 0.52 | 0.00 | 0.09 | 0.00 | 0.20 | 0.01 |
| PTPN7 | ENSG00000143851 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.08 | 0.02 | 0.00 | 0.10 | 0.00 | 0.13 | 0.00 | 0.08 | 0.01 | 0.05 | 0.01 | 0.15 | 0.06 | 0.08 | 0.02 | 0.04 | 0.01 | 0.06 | 0.05 | 0.01 | 0.00 | 0.20 | 0.01 | 0.18 | 0.02 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.23 | 0.01 | 0.33 | 0.07 | 0.06 | 0.00 | 0.14 | 0.02 | 0.23 | 0.03 | 0.12 | 0.12 | 0.08 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.00 | 0.01 | 0.03 | 0.01 | 0.09 | 0.00 | 0.20 | 0.01 |
| GDF7 | ENSG00000143869 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.06 | 0.02 | 0.10 | 0.03 | 0.03 | 0.02 | 0.07 | 0.04 | 0.03 | 0.04 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.04 | 0.10 | 0.01 | 0.00 | 0.05 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.20 | 0.14 | 0.09 | 0.01 | 0.10 | 0.03 | 0.28 | 0.03 | 0.03 | 0.10 | 0.18 | 0.01 | 0.00 | 0.00 | 0.02 | 0.07 | 0.01 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.01 | 0.04 |
| CALM2 | ENSG00000143933 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.08 | 0.01 | 0.25 | 0.01 | 0.04 | 0.01 | 0.05 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.05 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.29 | 0.04 | 0.06 | 0.00 | 0.10 | 0.03 | 0.20 | 0.02 | 0.05 | 0.06 | 0.12 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 |
| ASXL2 | ENSG00000143970 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 | 0.09 | 0.01 | 0.00 | 0.00 | 0.03 | 0.09 | 0.06 | 0.02 | 0.09 | 0.01 | 0.03 | 0.02 | 0.08 | 0.06 | 0.05 | 0.04 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.04 | 0.08 | 0.01 | 0.00 | 0.05 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.18 | 0.11 | 0.08 | 0.00 | 0.11 | 0.02 | 0.24 | 0.03 | 0.04 | 0.11 | 0.17 | 0.01 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.00 | 0.03 | 0.04 |
| DUSP11 | ENSG00000144048 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.01 | 0.13 | 0.01 | 0.05 | 0.00 | 0.07 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.15 | 0.04 | 0.03 | 0.00 | 0.04 | 0.01 | 0.10 | 0.02 | 0.06 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.04 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| THNSL2 | ENSG00000144115 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.08 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.02 | 0.08 | 0.02 | 0.06 | 0.01 | 0.09 | 0.01 | 0.01 | 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 | 0.02 | 0.10 | 0.04 | 0.04 | 0.01 | 0.04 | 0.02 | 0.08 | 0.02 | 0.19 | 0.04 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| C1QL2 | ENSG00000144119 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.11 | 0.01 | 0.11 | 0.01 | 0.30 | 0.03 | 0.07 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.11 | 0.13 | 0.03 | 0.00 | 0.04 | 0.02 | 0.09 | 0.00 | 0.13 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 |
| FBLN7 | ENSG00000144152 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.08 | 0.01 | 0.07 | 0.01 | 0.18 | 0.02 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.01 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.11 | 0.11 | 0.05 | 0.01 | 0.09 | 0.01 | 0.11 | 0.00 | 0.12 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| CNGA3 | ENSG00000144191 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.01 | 0.15 | 0.01 | 0.11 | 0.01 | 0.22 | 0.01 | 0.07 | 0.01 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.17 | 0.05 | 0.03 | 0.01 | 0.06 | 0.01 | 0.32 | 0.00 | 0.15 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 |
| LYG1 | ENSG00000144214 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.14 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.01 | 0.12 | 0.02 | 0.08 | 0.02 | 0.19 | 0.01 | 0.05 | 0.02 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.16 | 0.06 | 0.03 | 0.02 | 0.05 | 0.01 | 0.17 | 0.00 | 0.14 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| GPR17 | ENSG00000144230 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.06 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.02 | 0.06 | 0.01 | 0.07 | 0.06 | 0.03 | 0.05 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.11 | 0.17 | 0.03 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.14 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SCN1A | ENSG00000144285 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.06 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.10 | 0.02 | 0.08 | 0.01 | 0.11 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.01 | 0.06 | 0.05 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.31 | 0.05 | 0.06 | 0.01 | 0.05 | 0.02 | 0.03 | 0.00 | 0.05 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| METTL21A | ENSG00000144401 | 0.02 | 0.04 | 0.04 | 0.03 | 0.00 | 0.03 | 0.02 | 0.01 | 0.02 | 0.15 | 0.00 | 0.00 | 0.00 | 0.09 | 0.05 | 0.02 | 0.07 | 0.13 | 0.03 | 0.16 | 0.11 | 0.09 | 0.10 | 0.03 | 0.02 | 0.01 | 0.02 | 0.01 | 0.08 | 0.01 | 0.07 | 0.02 | 0.00 | 0.05 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.22 | 0.11 | 0.03 | 0.30 | 0.04 | 0.03 | 0.06 | 0.05 | 0.05 | 0.14 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 |
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