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 |
| SEC11A | ENSG00000140612 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.04 | 0.02 | 0.03 | 0.00 | 0.11 | 0.00 | 0.04 | 0.03 | 0.13 | 0.01 | 0.04 | 0.02 | 0.13 | 0.03 | 0.12 | 0.01 | 0.04 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.06 | 0.03 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.24 | 0.09 | 0.16 | 0.00 | 0.03 | 0.03 | 0.27 | 0.05 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.16 | 0.01 |
| SLC5A2 | ENSG00000140675 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.09 | 0.01 | 0.02 | 0.02 | 0.06 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.10 | 0.02 | 0.01 | 0.03 | 0.09 | 0.00 | 0.52 | 0.05 | 0.04 | 0.03 | 0.02 | 0.01 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| MYLK3 | ENSG00000140795 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.08 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.07 | 0.03 | 0.05 | 0.02 | 0.05 | 0.03 | 0.10 | 0.00 | 0.03 | 0.03 | 0.04 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.09 | 0.01 | 0.00 | 0.08 | 0.08 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.08 | 0.06 | 0.13 | 0.11 | 0.01 | 0.06 | 0.03 | 0.05 | 0.09 | 0.14 | 0.08 | 0.15 | 0.08 | 0.01 | 0.01 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 |
| ADAMTS18 | ENSG00000140873 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.22 | 0.11 | 0.04 | 0.03 | 0.03 | 0.00 | 0.13 | 0.03 | 0.07 | 0.03 | 0.05 | 0.02 | 0.03 | 0.05 | 0.02 | 0.04 | 0.04 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.04 | 0.01 | 0.06 | 0.05 | 0.01 | 0.06 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.04 | 0.06 | 0.04 | 0.30 | 0.04 | 0.04 | 0.02 | 0.08 | 0.01 | 0.24 | 0.04 | 0.05 | 0.00 | 0.09 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.05 |
| CTRL | ENSG00000141086 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.01 | 0.07 | 0.17 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.04 | 0.03 | 0.06 | 0.01 | 0.03 | 0.01 | 0.13 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.05 | 0.01 | 0.23 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.03 | 0.33 | 0.04 | 0.02 | 0.03 | 0.08 | 0.06 | 0.14 | 0.02 | 0.04 | 0.15 | 0.01 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 |
| DPEP3 | ENSG00000141096 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.01 | 0.07 | 0.17 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.05 | 0.03 | 0.06 | 0.01 | 0.03 | 0.01 | 0.13 | 0.01 | 0.04 | 0.04 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.04 | 0.05 | 0.01 | 0.23 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.03 | 0.05 | 0.03 | 0.33 | 0.04 | 0.02 | 0.02 | 0.08 | 0.06 | 0.14 | 0.02 | 0.05 | 0.15 | 0.01 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 |
| OR4D1 | ENSG00000141194 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.18 | 0.02 | 0.02 | 0.00 | 0.11 | 0.00 | 0.10 | 0.01 | 0.13 | 0.02 | 0.04 | 0.02 | 0.08 | 0.04 | 0.05 | 0.03 | 0.04 | 0.01 | 0.07 | 0.04 | 0.01 | 0.15 | 0.16 | 0.00 | 0.12 | 0.01 | 0.10 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.46 | 0.02 | 0.16 | 0.03 | 0.11 | 0.01 | 0.10 | 0.03 | 0.19 | 0.02 | 0.18 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.00 | 0.04 | 0.00 | 0.17 | 0.00 | 0.20 | 0.02 |
| SPACA3 | ENSG00000141316 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.20 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.07 | 0.01 | 0.05 | 0.04 | 0.04 | 0.02 | 0.18 | 0.03 | 0.16 | 0.02 | 0.05 | 0.01 | 0.07 | 0.01 | 0.05 | 0.02 | 0.05 | 0.03 | 0.09 | 0.01 | 0.01 | 0.07 | 0.00 | 0.14 | 0.00 | 0.00 | 0.16 | 0.08 | 0.05 | 0.19 | 0.00 | 0.03 | 0.06 | 0.06 | 0.11 | 0.12 | 0.04 | 0.16 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.03 | 0.02 | 0.03 |
| IMPA2 | ENSG00000141401 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.00 | 0.06 | 0.01 | 0.02 | 0.01 | 0.04 | 0.04 | 0.07 | 0.02 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.06 | 0.05 | 0.01 | 0.02 | 0.02 | 0.00 | 0.06 | 0.00 | 0.06 | 0.05 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 |
| ASXL3 | ENSG00000141431 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.09 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.13 | 0.03 | 0.11 | 0.02 | 0.07 | 0.03 | 0.12 | 0.05 | 0.08 | 0.06 | 0.01 | 0.02 | 0.03 | 0.01 | 0.02 | 0.04 | 0.03 | 0.01 | 0.04 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.26 | 0.07 | 0.01 | 0.00 | 0.05 | 0.01 | 0.09 | 0.00 | 0.11 | 0.06 | 0.05 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 |
| ADCYAP1 | ENSG00000141433 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.18 | 0.03 | 0.18 | 0.03 | 0.28 | 0.06 | 0.07 | 0.02 | 0.02 | 0.01 | 0.02 | 0.04 | 0.05 | 0.03 | 0.02 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.16 | 0.10 | 0.05 | 0.03 | 0.06 | 0.02 | 0.10 | 0.07 | 0.13 | 0.11 | 0.01 | 0.06 | 0.00 | 0.01 | 0.03 | 0.04 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.02 |
| MEP1B | ENSG00000141434 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.09 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.11 | 0.02 | 0.19 | 0.01 | 0.08 | 0.03 | 0.15 | 0.06 | 0.08 | 0.06 | 0.01 | 0.02 | 0.03 | 0.01 | 0.07 | 0.04 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.27 | 0.06 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.00 | 0.13 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SLC25A52 | ENSG00000141437 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.08 | 0.02 | 0.18 | 0.01 | 0.08 | 0.02 | 0.15 | 0.05 | 0.09 | 0.06 | 0.01 | 0.02 | 0.03 | 0.01 | 0.05 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.27 | 0.06 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.00 | 0.13 | 0.05 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SLC14A1 | ENSG00000141469 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.04 | 0.06 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 | 0.03 | 0.08 | 0.11 | 0.02 | 0.08 | 0.05 | 0.17 | 0.12 | 0.02 | 0.11 | 0.01 | 0.06 | 0.01 | 0.02 | 0.01 | 0.07 | 0.03 | 0.05 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.17 | 0.17 | 0.01 | 0.02 | 0.06 | 0.03 | 0.27 | 0.00 | 0.07 | 0.06 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 |
| ASGR1 | ENSG00000141505 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.21 | 0.05 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.05 | 0.01 | 0.02 | 0.02 | 0.03 | 0.03 | 0.04 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.03 | 0.00 | 0.15 | 0.01 | 0.08 | 0.02 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.07 | 0.12 | 0.03 | 0.00 | 0.03 | 0.04 | 0.02 | 0.09 | 0.16 | 0.06 | 0.36 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.07 | 0.00 | 0.00 | 0.02 | 0.04 |
| CBX8 | ENSG00000141570 | 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 | 0.40 | 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 |
| SAMD1 | ENSG00000141858 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.00 | 0.00 | 0.06 | 0.02 | 0.00 | 0.05 | 0.12 | 0.04 | 0.07 | 0.02 | 0.12 | 0.04 | 0.05 | 0.02 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.07 | 0.06 | 0.00 | 0.03 | 0.18 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.03 | 0.85 | 0.06 | 0.09 | 0.01 | 0.20 | 0.02 | 0.21 | 0.11 | 0.25 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 |
| PRDM15 | ENSG00000141956 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.08 | 0.01 | 0.07 | 0.02 | 0.09 | 0.03 | 0.08 | 0.01 | 0.01 | 0.01 | 0.08 | 0.01 | 0.01 | 0.02 | 0.02 | 0.07 | 0.03 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.11 | 0.17 | 0.06 | 0.04 | 0.04 | 0.01 | 0.07 | 0.03 | 0.06 | 0.07 | 0.04 | 0.00 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 |
| SOD1 | ENSG00000142168 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.04 | 0.03 | 0.04 | 0.00 | 0.02 | 0.05 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.10 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.10 | 0.08 | 0.02 | 0.05 | 0.02 | 0.02 | 0.00 | 0.05 | 0.12 | 0.04 | 0.02 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.03 | 0.00 | 0.02 | 0.01 |
| SIK1 | ENSG00000142178 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.05 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 | 0.03 | 0.06 | 0.01 | 0.05 | 0.03 | 0.07 | 0.02 | 0.07 | 0.01 | 0.02 | 0.01 | 0.08 | 0.01 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.16 | 0.17 | 0.04 | 0.02 | 0.04 | 0.02 | 0.13 | 0.03 | 0.08 | 0.08 | 0.04 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 |
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