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 |
| FGF23 | ENSG00000118972 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.09 | 0.03 | 0.01 | 0.00 | 0.02 | 0.01 | 0.06 | 0.07 | 0.19 | 0.01 | 0.15 | 0.01 | 0.11 | 0.03 | 0.06 | 0.06 | 0.17 | 0.01 | 0.15 | 0.02 | 0.10 | 0.05 | 0.02 | 0.04 | 0.14 | 0.05 | 0.07 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.13 | 0.04 | 0.39 | 0.08 | 0.05 | 0.02 | 0.07 | 0.02 | 0.34 | 0.02 | 0.20 | 0.11 | 0.57 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.19 | 0.00 | 0.13 | 0.01 | 0.00 | 0.01 | 0.05 | 0.04 |
| C2orf40 | ENSG00000119147 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.10 | 0.01 | 0.07 | 0.01 | 0.23 | 0.01 | 0.11 | 0.02 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.11 | 0.09 | 0.03 | 0.02 | 0.03 | 0.01 | 0.06 | 0.00 | 0.12 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 |
| HSDL2 | ENSG00000119471 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.04 | 0.05 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.04 | 0.01 | 0.05 | 0.00 | 0.11 | 0.02 | 0.05 | 0.03 | 0.00 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.06 | 0.04 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.11 | 0.02 | 0.00 | 0.01 | 0.04 | 0.01 | 0.21 | 0.07 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 |
| CSF3R | ENSG00000119535 | 0.00 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.06 | 0.00 | 0.00 | 0.11 | 0.05 | 0.07 | 0.03 | 0.06 | 0.04 | 0.05 | 0.02 | 0.07 | 0.07 | 0.06 | 0.04 | 0.02 | 0.04 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.12 | 0.00 | 0.33 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.00 | 0.07 | 0.06 | 0.56 | 0.11 | 0.05 | 0.03 | 0.08 | 0.04 | 0.14 | 0.04 | 0.10 | 0.04 | 0.06 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.10 | 0.04 | 0.03 |
| KDSR | ENSG00000119537 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.09 | 0.04 | 0.06 | 0.02 | 0.14 | 0.03 | 0.20 | 0.02 | 0.16 | 0.00 | 0.12 | 0.01 | 0.09 | 0.00 | 0.08 | 0.02 | 0.07 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.05 | 0.09 | 0.32 | 0.01 | 0.03 | 0.01 | 0.07 | 0.01 | 0.11 | 0.12 | 0.07 | 0.00 | 0.07 | 0.00 | 0.00 | 0.17 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.01 |
| PGF | ENSG00000119630 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.05 | 0.04 | 0.00 | 0.01 | 0.00 | 0.06 | 0.04 | 0.05 | 0.05 | 0.03 | 0.05 | 0.01 | 0.06 | 0.02 | 0.03 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.01 | 0.01 | 0.10 | 0.00 | 0.28 | 0.06 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.10 | 0.14 | 0.19 | 0.05 | 0.03 | 0.03 | 0.02 | 0.09 | 0.06 | 0.08 | 0.11 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.01 | 0.09 | 0.03 | 0.00 | 0.00 | 0.05 |
| MLH3 | ENSG00000119684 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.04 | 0.05 | 0.04 | 0.00 | 0.01 | 0.00 | 0.06 | 0.04 | 0.05 | 0.05 | 0.03 | 0.05 | 0.01 | 0.07 | 0.02 | 0.06 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.01 | 0.01 | 0.10 | 0.00 | 0.28 | 0.12 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.10 | 0.14 | 0.19 | 0.05 | 0.03 | 0.04 | 0.02 | 0.04 | 0.06 | 0.08 | 0.12 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 |
| FLVCR2 | ENSG00000119686 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.05 | 0.06 | 0.00 | 0.01 | 0.00 | 0.06 | 0.04 | 0.06 | 0.06 | 0.03 | 0.05 | 0.02 | 0.07 | 0.02 | 0.03 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.03 | 0.02 | 0.02 | 0.10 | 0.00 | 0.26 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.10 | 0.13 | 0.18 | 0.06 | 0.03 | 0.03 | 0.02 | 0.04 | 0.08 | 0.07 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 |
| ABCD4 | ENSG00000119688 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.05 | 0.05 | 0.04 | 0.00 | 0.01 | 0.00 | 0.07 | 0.04 | 0.04 | 0.05 | 0.03 | 0.05 | 0.01 | 0.05 | 0.02 | 0.02 | 0.05 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.28 | 0.00 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.10 | 0.12 | 0.20 | 0.05 | 0.03 | 0.02 | 0.02 | 0.08 | 0.06 | 0.07 | 0.12 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 |
| TGFB3 | ENSG00000119699 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.06 | 0.06 | 0.00 | 0.01 | 0.00 | 0.06 | 0.04 | 0.06 | 0.05 | 0.03 | 0.05 | 0.02 | 0.06 | 0.02 | 0.04 | 0.04 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.10 | 0.00 | 0.26 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.02 | 0.10 | 0.12 | 0.18 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.08 | 0.09 | 0.14 | 0.03 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.12 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 |
| ALDH6A1 | ENSG00000119711 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.05 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.08 | 0.04 | 0.05 | 0.04 | 0.03 | 0.04 | 0.01 | 0.05 | 0.02 | 0.02 | 0.05 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.02 | 0.09 | 0.00 | 0.33 | 0.01 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.10 | 0.11 | 0.19 | 0.05 | 0.03 | 0.02 | 0.02 | 0.09 | 0.06 | 0.07 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.12 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.05 |
| GPR75 | ENSG00000119737 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.10 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.01 | 0.25 | 0.01 | 0.04 | 0.01 | 0.06 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.03 | 0.01 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.01 | 0.25 | 0.04 | 0.03 | 0.02 | 0.05 | 0.01 | 0.04 | 0.02 | 0.08 | 0.06 | 0.07 | 0.02 | 0.00 | 0.00 | 0.17 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 |
| KLHL29 | ENSG00000119771 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.06 | 0.02 | 0.09 | 0.03 | 0.03 | 0.02 | 0.06 | 0.05 | 0.03 | 0.03 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.04 | 0.09 | 0.02 | 0.00 | 0.05 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.19 | 0.13 | 0.08 | 0.00 | 0.11 | 0.03 | 0.22 | 0.05 | 0.04 | 0.10 | 0.17 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.00 | 0.03 | 0.04 |
| FKBP1B | ENSG00000119782 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.05 | 0.01 | 0.08 | 0.02 | 0.04 | 0.02 | 0.06 | 0.05 | 0.03 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.08 | 0.01 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.17 | 0.12 | 0.08 | 0.00 | 0.11 | 0.02 | 0.30 | 0.03 | 0.05 | 0.10 | 0.17 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.03 | 0.05 | 0.00 | 0.02 | 0.04 |
| TECTB | ENSG00000119913 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.01 | 0.10 | 0.00 | 0.02 | 0.01 | 0.20 | 0.03 | 0.03 | 0.04 | 0.07 | 0.01 | 0.03 | 0.03 | 0.07 | 0.07 | 0.06 | 0.01 | 0.08 | 0.01 | 0.07 | 0.01 | 0.01 | 0.06 | 0.10 | 0.11 | 0.21 | 0.07 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.10 | 0.17 | 0.22 | 0.01 | 0.07 | 0.04 | 0.07 | 0.18 | 0.13 | 0.04 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.11 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.05 |
| ELOVL3 | ENSG00000119915 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.10 | 0.01 | 0.09 | 0.00 | 0.02 | 0.00 | 0.16 | 0.01 | 0.03 | 0.01 | 0.07 | 0.01 | 0.05 | 0.05 | 0.07 | 0.02 | 0.08 | 0.00 | 0.10 | 0.01 | 0.07 | 0.03 | 0.03 | 0.02 | 0.07 | 0.11 | 0.14 | 0.08 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.08 | 0.08 | 0.31 | 0.01 | 0.07 | 0.03 | 0.08 | 0.05 | 0.11 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 |
| SMNDC1 | ENSG00000119953 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.01 | 0.11 | 0.00 | 0.02 | 0.01 | 0.20 | 0.02 | 0.03 | 0.03 | 0.07 | 0.01 | 0.03 | 0.03 | 0.07 | 0.05 | 0.07 | 0.00 | 0.07 | 0.01 | 0.07 | 0.01 | 0.01 | 0.02 | 0.08 | 0.11 | 0.21 | 0.07 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.10 | 0.13 | 0.24 | 0.01 | 0.07 | 0.03 | 0.07 | 0.03 | 0.13 | 0.06 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.08 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 |
| PRLHR | ENSG00000119973 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.09 | 0.00 | 0.02 | 0.01 | 0.19 | 0.02 | 0.03 | 0.04 | 0.06 | 0.01 | 0.03 | 0.04 | 0.06 | 0.07 | 0.06 | 0.01 | 0.06 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.11 | 0.02 | 0.25 | 0.11 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.10 | 0.16 | 0.22 | 0.01 | 0.06 | 0.05 | 0.06 | 0.04 | 0.05 | 0.03 | 0.06 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.12 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 |
| CRHR1 | ENSG00000120088 | 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 |
| DUSP1 | ENSG00000120129 | 0.33 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.03 | 0.10 | 0.00 | 0.00 | 0.02 | 0.05 | 0.11 | 0.04 | 0.02 | 0.05 | 0.02 | 0.05 | 0.07 | 0.02 | 0.03 | 0.04 | 0.02 | 0.01 | 0.04 | 0.04 | 0.03 | 0.02 | 0.16 | 0.02 | 0.05 | 0.01 | 0.38 | 0.02 | 0.00 | 0.03 | 0.01 | 0.00 | 0.09 | 0.04 | 0.23 | 0.14 | 0.03 | 0.03 | 0.05 | 0.02 | 0.21 | 0.01 | 0.14 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.07 | 0.02 | 0.04 | 0.04 | 0.00 | 0.04 | 0.10 |
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