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 |
| CASP3 | ENSG00000164305 | 0.00 | 0.03 | 0.00 | 0.01 | 0.10 | 0.04 | 0.03 | 0.03 | 0.04 | 0.17 | 0.00 | 0.02 | 0.00 | 0.07 | 0.02 | 0.13 | 0.03 | 0.19 | 0.03 | 0.13 | 0.07 | 0.11 | 0.02 | 0.24 | 0.01 | 0.14 | 0.02 | 0.13 | 0.00 | 0.06 | 0.07 | 0.23 | 0.00 | 0.35 | 0.20 | 0.18 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.12 | 0.07 | 0.38 | 0.04 | 0.12 | 0.03 | 0.09 | 0.09 | 0.16 | 0.04 | 0.32 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.16 | 0.00 | 0.10 | 0.00 | 0.09 | 0.00 | 0.00 | 0.05 | 0.10 |
| ERAP1 | ENSG00000164307 | 0.06 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.16 | 0.02 | 0.09 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.02 | 0.08 | 0.00 | 0.07 | 0.03 | 0.10 | 0.01 | 0.12 | 0.00 | 0.12 | 0.01 | 0.02 | 0.00 | 0.04 | 0.03 | 0.04 | 0.00 | 0.07 | 0.12 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.07 | 0.05 | 0.50 | 0.00 | 0.05 | 0.01 | 0.07 | 0.05 | 0.19 | 0.05 | 0.04 | 0.01 | 0.00 | 0.00 | 0.07 | 0.04 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.03 |
| EGFLAM | ENSG00000164318 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.03 | 0.13 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.21 | 0.01 | 0.23 | 0.01 | 0.08 | 0.00 | 0.15 | 0.01 | 0.18 | 0.01 | 0.05 | 0.01 | 0.05 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.20 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.02 | 0.23 | 0.02 | 0.07 | 0.00 | 0.08 | 0.01 | 0.15 | 0.03 | 0.31 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.21 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.19 | 0.02 |
| CARTPT | ENSG00000164326 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.21 | 0.01 | 0.13 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.07 | 0.01 | 0.09 | 0.01 | 0.07 | 0.01 | 0.16 | 0.02 | 0.13 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.07 | 0.00 | 0.04 | 0.00 | 0.13 | 0.05 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.10 | 0.02 | 0.72 | 0.00 | 0.06 | 0.02 | 0.11 | 0.04 | 0.42 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 |
| TLR3 | ENSG00000164342 | 0.00 | 0.03 | 0.00 | 0.02 | 0.10 | 0.04 | 0.03 | 0.03 | 0.03 | 0.19 | 0.00 | 0.02 | 0.00 | 0.07 | 0.02 | 0.12 | 0.04 | 0.19 | 0.03 | 0.16 | 0.07 | 0.12 | 0.03 | 0.22 | 0.01 | 0.12 | 0.02 | 0.10 | 0.00 | 0.05 | 0.07 | 0.20 | 0.00 | 0.35 | 0.19 | 0.18 | 0.03 | 0.06 | 0.00 | 0.00 | 0.05 | 0.12 | 0.09 | 0.40 | 0.05 | 0.16 | 0.03 | 0.09 | 0.13 | 0.16 | 0.06 | 0.33 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.12 | 0.00 | 0.12 | 0.00 | 0.09 | 0.00 | 0.00 | 0.05 | 0.10 |
| KLKB1 | ENSG00000164344 | 0.00 | 0.03 | 0.00 | 0.02 | 0.10 | 0.04 | 0.03 | 0.03 | 0.03 | 0.19 | 0.00 | 0.02 | 0.00 | 0.07 | 0.02 | 0.12 | 0.03 | 0.21 | 0.03 | 0.17 | 0.07 | 0.12 | 0.03 | 0.22 | 0.01 | 0.12 | 0.02 | 0.10 | 0.00 | 0.06 | 0.07 | 0.20 | 0.00 | 0.35 | 0.19 | 0.18 | 0.02 | 0.06 | 0.00 | 0.00 | 0.05 | 0.12 | 0.08 | 0.39 | 0.06 | 0.18 | 0.03 | 0.09 | 0.13 | 0.16 | 0.06 | 0.33 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.12 | 0.00 | 0.12 | 0.00 | 0.09 | 0.00 | 0.00 | 0.05 | 0.10 |
| IL3 | ENSG00000164399 | 0.28 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.07 | 0.01 | 0.05 | 0.04 | 0.06 | 0.02 | 0.11 | 0.01 | 0.04 | 0.02 | 0.05 | 0.01 | 0.04 | 0.07 | 0.04 | 0.09 | 0.01 | 0.22 | 0.03 | 0.00 | 0.03 | 0.01 | 0.00 | 0.03 | 0.05 | 0.12 | 0.19 | 0.02 | 0.04 | 0.01 | 0.02 | 0.10 | 0.04 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.09 |
| CSF2 | ENSG00000164400 | 0.28 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.07 | 0.00 | 0.07 | 0.01 | 0.05 | 0.04 | 0.06 | 0.02 | 0.11 | 0.01 | 0.04 | 0.02 | 0.04 | 0.01 | 0.04 | 0.07 | 0.04 | 0.09 | 0.01 | 0.22 | 0.03 | 0.00 | 0.03 | 0.01 | 0.00 | 0.03 | 0.05 | 0.12 | 0.19 | 0.02 | 0.04 | 0.01 | 0.02 | 0.10 | 0.04 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.09 | 0.04 | 0.02 | 0.00 | 0.03 | 0.02 | 0.03 | 0.00 | 0.03 | 0.01 | 0.09 |
| GDF9 | ENSG00000164404 | 0.28 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.06 | 0.01 | 0.05 | 0.03 | 0.06 | 0.02 | 0.10 | 0.01 | 0.05 | 0.02 | 0.05 | 0.01 | 0.04 | 0.11 | 0.04 | 0.09 | 0.01 | 0.32 | 0.02 | 0.00 | 0.04 | 0.01 | 0.00 | 0.03 | 0.04 | 0.13 | 0.19 | 0.02 | 0.03 | 0.01 | 0.02 | 0.15 | 0.04 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.04 | 0.02 | 0.02 | 0.00 | 0.03 | 0.01 | 0.09 |
| LEAP2 | ENSG00000164406 | 0.28 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 | 0.07 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.08 | 0.00 | 0.06 | 0.01 | 0.06 | 0.03 | 0.06 | 0.02 | 0.10 | 0.01 | 0.05 | 0.02 | 0.05 | 0.01 | 0.04 | 0.11 | 0.04 | 0.09 | 0.01 | 0.32 | 0.02 | 0.00 | 0.04 | 0.01 | 0.00 | 0.03 | 0.04 | 0.13 | 0.19 | 0.02 | 0.03 | 0.01 | 0.02 | 0.15 | 0.04 | 0.04 | 0.06 | 0.01 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.04 | 0.02 | 0.02 | 0.00 | 0.03 | 0.01 | 0.09 |
| FABP7 | ENSG00000164434 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.04 | 0.06 | 0.00 | 0.01 | 0.02 | 0.14 | 0.02 | 0.05 | 0.04 | 0.04 | 0.03 | 0.02 | 0.13 | 0.01 | 0.04 | 0.04 | 0.02 | 0.02 | 0.01 | 0.03 | 0.00 | 0.03 | 0.01 | 0.07 | 0.06 | 0.14 | 0.07 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.06 | 0.10 | 0.24 | 0.01 | 0.02 | 0.04 | 0.02 | 0.09 | 0.03 | 0.19 | 0.07 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.19 | 0.00 | 0.04 | 0.00 | 0.08 | 0.04 | 0.03 | 0.02 | 0.12 |
| IL22RA2 | ENSG00000164485 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.14 | 0.03 | 0.04 | 0.05 | 0.03 | 0.07 | 0.02 | 0.13 | 0.01 | 0.11 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.03 | 0.02 | 0.01 | 0.08 | 0.00 | 0.10 | 0.10 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.11 | 0.06 | 0.08 | 0.28 | 0.01 | 0.04 | 0.05 | 0.02 | 0.08 | 0.03 | 0.40 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.00 | 0.04 | 0.01 | 0.11 | 0.00 | 0.09 | 0.01 | 0.14 |
| IL31RA | ENSG00000164509 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.23 | 0.07 | 0.13 | 0.00 | 0.00 | 0.01 | 0.01 | 0.07 | 0.06 | 0.03 | 0.10 | 0.03 | 0.09 | 0.02 | 0.13 | 0.02 | 0.10 | 0.02 | 0.06 | 0.01 | 0.06 | 0.00 | 0.05 | 0.02 | 0.02 | 0.00 | 0.10 | 0.04 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.10 | 0.04 | 0.52 | 0.04 | 0.08 | 0.01 | 0.12 | 0.01 | 0.32 | 0.08 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 |
| PI16 | ENSG00000164530 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.11 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.01 | 0.07 | 0.04 | 0.02 | 0.03 | 0.18 | 0.03 | 0.08 | 0.03 | 0.04 | 0.01 | 0.06 | 0.01 | 0.01 | 0.01 | 0.04 | 0.03 | 0.05 | 0.03 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.33 | 0.04 | 0.08 | 0.00 | 0.08 | 0.01 | 0.29 | 0.03 | 0.06 | 0.06 | 0.05 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.10 | 0.00 | 0.10 | 0.01 |
| DAGLB | ENSG00000164535 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.15 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.11 | 0.01 | 0.13 | 0.02 | 0.10 | 0.01 | 0.21 | 0.02 | 0.14 | 0.01 | 0.05 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.07 | 0.01 | 0.01 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.12 | 0.39 | 0.04 | 0.02 | 0.04 | 0.05 | 0.09 | 0.03 | 0.22 | 0.04 | 0.18 | 0.01 | 0.00 | 0.01 | 0.10 | 0.00 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.16 | 0.01 |
| STK17A | ENSG00000164543 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.09 | 0.02 | 0.05 | 0.01 | 0.10 | 0.02 | 0.04 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.09 | 0.07 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.00 | 0.07 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 |
| HCN1 | ENSG00000164588 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.12 | 0.14 | 0.10 | 0.00 | 0.00 | 0.01 | 0.01 | 0.18 | 0.07 | 0.25 | 0.09 | 0.10 | 0.09 | 0.24 | 0.10 | 0.16 | 0.08 | 0.05 | 0.03 | 0.07 | 0.02 | 0.02 | 0.04 | 0.03 | 0.01 | 0.00 | 0.10 | 0.21 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.08 | 0.08 | 0.20 | 0.28 | 0.08 | 0.06 | 0.05 | 0.10 | 0.16 | 0.26 | 0.22 | 0.06 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.13 | 0.03 |
| GPR85 | ENSG00000164604 | 0.01 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.07 | 0.02 | 0.00 | 0.01 | 0.03 | 0.03 | 0.09 | 0.03 | 0.11 | 0.05 | 0.10 | 0.05 | 0.26 | 0.14 | 0.08 | 0.05 | 0.01 | 0.01 | 0.02 | 0.01 | 0.01 | 0.03 | 0.08 | 0.03 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.04 | 0.26 | 0.06 | 0.04 | 0.05 | 0.03 | 0.03 | 0.08 | 0.11 | 0.15 | 0.02 | 0.03 | 0.02 | 0.00 | 0.03 | 0.09 | 0.02 | 0.09 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.12 | 0.02 |
| SLC29A4 | ENSG00000164638 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.14 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.09 | 0.02 | 0.15 | 0.02 | 0.11 | 0.01 | 0.20 | 0.02 | 0.16 | 0.02 | 0.05 | 0.00 | 0.04 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.01 | 0.01 | 0.12 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.05 | 0.08 | 0.41 | 0.06 | 0.04 | 0.05 | 0.07 | 0.16 | 0.03 | 0.18 | 0.05 | 0.14 | 0.01 | 0.00 | 0.01 | 0.10 | 0.00 | 0.01 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.16 | 0.01 |
| STEAP1 | ENSG00000164647 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.07 | 0.01 | 0.21 | 0.02 | 0.17 | 0.01 | 0.63 | 0.07 | 0.30 | 0.03 | 0.03 | 0.01 | 0.01 | 0.00 | 0.15 | 0.00 | 0.11 | 0.02 | 0.04 | 0.01 | 0.10 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.15 | 0.06 | 0.07 | 0.01 | 0.04 | 0.03 | 0.08 | 0.03 | 0.12 | 0.05 | 0.13 | 0.00 | 0.00 | 0.01 | 0.13 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
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