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 |
| CLCA3P | ENSG00000153923 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.30 | 0.03 | 0.09 | 0.05 | 0.05 | 0.01 | 0.06 | 0.01 | 0.07 | 0.01 | 0.07 | 0.00 | 0.07 | 0.01 | 0.08 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.10 | 0.04 | 0.07 | 0.00 | 0.23 | 0.00 | 0.00 | 0.04 | 0.09 | 0.13 | 0.19 | 0.02 | 0.04 | 0.01 | 0.03 | 0.10 | 0.05 | 0.12 | 0.06 | 0.03 | 0.05 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.05 | 0.03 | 0.03 | 0.02 | 0.10 |
| CHST9 | ENSG00000154080 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.08 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 | 0.13 | 0.02 | 0.23 | 0.03 | 0.17 | 0.05 | 0.20 | 0.07 | 0.11 | 0.06 | 0.01 | 0.03 | 0.02 | 0.04 | 0.06 | 0.05 | 0.00 | 0.01 | 0.00 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.31 | 0.05 | 0.06 | 0.02 | 0.09 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.00 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| THY1 | ENSG00000154096 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.02 | 0.01 | 0.08 | 0.03 | 0.11 | 0.00 | 0.00 | 0.11 | 0.06 | 0.05 | 0.08 | 0.05 | 0.09 | 0.04 | 0.16 | 0.03 | 0.12 | 0.06 | 0.07 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.17 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.22 | 0.16 | 0.15 | 0.04 | 0.31 | 0.05 | 0.05 | 0.11 | 0.17 | 0.04 | 0.24 | 0.00 | 0.15 | 0.03 | 0.01 | 0.13 | 0.05 | 0.06 | 0.01 | 0.02 | 0.01 | 0.01 | 0.07 | 0.00 | 0.27 |
| GPR15 | ENSG00000154165 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.02 | 0.17 | 0.03 | 0.06 | 0.01 | 0.10 | 0.03 | 0.05 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.12 | 0.10 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.22 | 0.04 | 0.05 | 0.01 | 0.04 | 0.00 | 0.18 | 0.08 | 0.07 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| ABI3BP | ENSG00000154175 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.02 | 0.18 | 0.03 | 0.06 | 0.01 | 0.08 | 0.04 | 0.06 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.05 | 0.10 | 0.11 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.06 | 0.02 | 0.21 | 0.04 | 0.07 | 0.02 | 0.06 | 0.01 | 0.22 | 0.08 | 0.11 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.03 | 0.01 |
| ANGPT1 | ENSG00000154188 | 0.01 | 0.00 | 0.01 | 0.00 | 0.20 | 0.00 | 0.07 | 0.02 | 0.34 | 0.01 | 0.04 | 0.00 | 0.02 | 0.06 | 0.18 | 0.01 | 0.29 | 0.01 | 0.17 | 0.00 | 0.34 | 0.00 | 0.22 | 0.00 | 0.14 | 0.00 | 0.16 | 0.00 | 0.06 | 0.01 | 0.33 | 0.00 | 0.25 | 0.01 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.47 | 0.01 | 0.88 | 0.07 | 0.14 | 0.00 | 0.15 | 0.01 | 0.32 | 0.00 | 0.14 | 0.06 | 0.06 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.17 | 0.00 | 0.02 | 0.01 | 0.43 | 0.00 | 0.15 | 0.01 |
| UCHL1 | ENSG00000154277 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.02 | 0.06 | 0.03 | 0.02 | 0.02 | 0.07 | 0.03 | 0.02 | 0.03 | 0.01 | 0.01 | 0.02 | 0.05 | 0.02 | 0.01 | 0.05 | 0.01 | 0.00 | 0.07 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.10 | 0.07 | 0.00 | 0.02 | 0.03 | 0.03 | 0.06 | 0.07 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.03 | 0.01 |
| WNT3A | ENSG00000154342 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.10 | 0.05 | 0.02 | 0.02 | 0.05 | 0.03 | 0.09 | 0.01 | 0.12 | 0.01 | 0.06 | 0.00 | 0.20 | 0.04 | 0.09 | 0.02 | 0.03 | 0.02 | 0.05 | 0.01 | 0.01 | 0.01 | 0.14 | 0.02 | 0.23 | 0.02 | 0.04 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.23 | 0.02 | 0.41 | 0.05 | 0.08 | 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 |
| GPR26 | ENSG00000154478 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.04 | 0.10 | 0.00 | 0.02 | 0.02 | 0.15 | 0.03 | 0.03 | 0.05 | 0.06 | 0.02 | 0.03 | 0.06 | 0.05 | 0.14 | 0.05 | 0.01 | 0.05 | 0.01 | 0.06 | 0.03 | 0.01 | 0.01 | 0.10 | 0.14 | 0.17 | 0.11 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.08 | 0.09 | 0.23 | 0.19 | 0.02 | 0.05 | 0.05 | 0.06 | 0.06 | 0.04 | 0.07 | 0.08 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.13 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.04 |
| MMP21 | ENSG00000154485 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.06 | 0.03 | 0.09 | 0.00 | 0.02 | 0.02 | 0.15 | 0.04 | 0.03 | 0.06 | 0.06 | 0.01 | 0.03 | 0.08 | 0.06 | 0.13 | 0.06 | 0.01 | 0.06 | 0.01 | 0.05 | 0.01 | 0.01 | 0.02 | 0.10 | 0.14 | 0.11 | 0.14 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.09 | 0.25 | 0.18 | 0.02 | 0.05 | 0.05 | 0.05 | 0.17 | 0.04 | 0.06 | 0.06 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.14 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.04 |
| CNTNAP3B | ENSG00000154529 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| CXXC1 | ENSG00000154832 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.10 | 0.01 | 0.04 | 0.01 | 0.08 | 0.01 | 0.21 | 0.03 | 0.18 | 0.01 | 0.07 | 0.00 | 0.08 | 0.01 | 0.08 | 0.02 | 0.07 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.06 | 0.26 | 0.01 | 0.04 | 0.02 | 0.04 | 0.01 | 0.07 | 0.07 | 0.06 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.00 |
| DKK2 | ENSG00000155011 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.04 | 0.03 | 0.05 | 0.01 | 0.02 | 0.01 | 0.07 | 0.02 | 0.04 | 0.00 | 0.03 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.13 | 0.00 | 0.11 | 0.04 | 0.04 | 0.03 | 0.06 | 0.00 | 0.00 | 0.04 | 0.05 | 0.03 | 0.29 | 0.01 | 0.02 | 0.01 | 0.04 | 0.11 | 0.11 | 0.04 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 |
| CYP2U1 | ENSG00000155016 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.05 | 0.01 | 0.02 | 0.02 | 0.07 | 0.02 | 0.05 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.12 | 0.00 | 0.11 | 0.07 | 0.04 | 0.03 | 0.03 | 0.00 | 0.00 | 0.04 | 0.06 | 0.03 | 0.28 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.14 | 0.06 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.04 |
| CNTNAP5 | ENSG00000155052 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.14 | 0.06 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.12 | 0.02 | 0.07 | 0.01 | 0.14 | 0.06 | 0.05 | 0.04 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.01 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.08 | 0.16 | 0.03 | 0.01 | 0.03 | 0.01 | 0.09 | 0.00 | 0.16 | 0.02 | 0.04 | 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 |
| OR4K1 | ENSG00000155249 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.04 | 0.20 | 0.07 | 0.09 | 0.06 | 0.11 | 0.07 | 0.07 | 0.04 | 0.03 | 0.02 | 0.01 | 0.09 | 0.01 | 0.04 | 0.08 | 0.00 | 0.00 | 0.02 | 0.13 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.10 | 0.03 | 0.40 | 0.12 | 0.07 | 0.02 | 0.08 | 0.03 | 0.21 | 0.08 | 0.17 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| GPR78 | ENSG00000155269 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.04 | 0.04 | 0.03 | 0.06 | 0.09 | 0.09 | 0.05 | 0.04 | 0.02 | 0.03 | 0.03 | 0.03 | 0.02 | 0.01 | 0.03 | 0.04 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.04 | 0.23 | 0.06 | 0.01 | 0.03 | 0.05 | 0.03 | 0.13 | 0.00 | 0.06 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.06 | 0.03 |
| SLC25A28 | ENSG00000155287 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.11 | 0.02 | 0.10 | 0.00 | 0.02 | 0.00 | 0.17 | 0.01 | 0.03 | 0.02 | 0.07 | 0.00 | 0.06 | 0.02 | 0.08 | 0.01 | 0.09 | 0.00 | 0.10 | 0.00 | 0.07 | 0.01 | 0.03 | 0.03 | 0.06 | 0.11 | 0.14 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.08 | 0.05 | 0.34 | 0.01 | 0.07 | 0.02 | 0.09 | 0.03 | 0.09 | 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 |
| VSIG4 | ENSG00000155659 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.04 | 0.02 | 0.02 | 0.11 | 0.03 | 0.02 | 0.03 | 0.03 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.20 | 0.04 | 0.04 | 0.01 | 0.05 | 0.01 | 0.10 | 0.00 | 0.18 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 |
| KDM8 | ENSG00000155666 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.13 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.01 | 0.09 | 0.01 | 0.04 | 0.01 | 0.05 | 0.00 | 0.05 | 0.00 | 0.04 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.07 | 0.03 | 0.02 | 0.01 | 0.06 | 0.00 | 0.28 | 0.03 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
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