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 |
| DEFB126 | ENSG00000125788 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.05 | 0.14 | 0.03 | 0.03 | 0.03 | 0.10 | 0.03 | 0.05 | 0.02 | 0.04 | 0.05 | 0.09 | 0.09 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.03 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.08 | 0.33 | 0.10 | 0.03 | 0.03 | 0.07 | 0.03 | 0.11 | 0.10 | 0.08 | 0.09 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.04 |
| CD93 | ENSG00000125810 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.08 | 0.01 | 0.06 | 0.03 | 0.05 | 0.02 | 0.07 | 0.03 | 0.06 | 0.01 | 0.05 | 0.01 | 0.03 | 0.02 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.08 | 0.05 | 0.04 | 0.02 | 0.02 | 0.01 | 0.05 | 0.00 | 0.07 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 |
| CST8 | ENSG00000125815 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.06 | 0.03 | 0.04 | 0.02 | 0.07 | 0.03 | 0.05 | 0.01 | 0.05 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.09 | 0.05 | 0.04 | 0.02 | 0.03 | 0.01 | 0.05 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| TMX4 | ENSG00000125827 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.03 | 0.15 | 0.01 | 0.05 | 0.02 | 0.07 | 0.02 | 0.04 | 0.01 | 0.03 | 0.05 | 0.06 | 0.07 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.03 | 0.07 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.05 | 0.23 | 0.07 | 0.06 | 0.01 | 0.06 | 0.01 | 0.04 | 0.12 | 0.07 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 |
| CST11 | ENSG00000125831 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.06 | 0.03 | 0.04 | 0.02 | 0.07 | 0.03 | 0.05 | 0.01 | 0.05 | 0.01 | 0.03 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.09 | 0.05 | 0.04 | 0.02 | 0.03 | 0.01 | 0.05 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| GFRA4 | ENSG00000125861 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.03 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.04 | 0.13 | 0.01 | 0.03 | 0.02 | 0.07 | 0.03 | 0.05 | 0.01 | 0.06 | 0.04 | 0.05 | 0.08 | 0.00 | 0.03 | 0.05 | 0.01 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.05 | 0.29 | 0.07 | 0.04 | 0.01 | 0.10 | 0.03 | 0.09 | 0.06 | 0.09 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 |
| OTOR | ENSG00000125879 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.02 | 0.08 | 0.00 | 0.05 | 0.02 | 0.04 | 0.02 | 0.02 | 0.02 | 0.07 | 0.04 | 0.06 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 | 0.12 | 0.06 | 0.03 | 0.03 | 0.02 | 0.02 | 0.01 | 0.02 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 |
| S1PR4 | ENSG00000125910 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.04 | 0.13 | 0.02 | 0.00 | 0.03 | 0.10 | 0.03 | 0.09 | 0.02 | 0.12 | 0.02 | 0.13 | 0.07 | 0.16 | 0.00 | 0.09 | 0.01 | 0.05 | 0.01 | 0.10 | 0.01 | 0.06 | 0.01 | 0.14 | 0.00 | 0.03 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.13 | 0.02 | 0.90 | 0.09 | 0.18 | 0.01 | 0.27 | 0.07 | 0.75 | 0.13 | 0.13 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.05 | 0.02 | 0.01 | 0.02 | 0.03 | 0.07 |
| GRPR | ENSG00000126010 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.11 | 0.04 | 0.04 | 0.02 | 0.06 | 0.04 | 0.05 | 0.02 | 0.00 | 0.01 | 0.12 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.13 | 0.16 | 0.05 | 0.01 | 0.04 | 0.02 | 0.08 | 0.07 | 0.15 | 0.05 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 |
| PSMB2 | ENSG00000126067 | 0.00 | 0.03 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.06 | 0.00 | 0.00 | 0.11 | 0.05 | 0.07 | 0.04 | 0.04 | 0.04 | 0.05 | 0.02 | 0.06 | 0.06 | 0.05 | 0.04 | 0.02 | 0.06 | 0.01 | 0.05 | 0.02 | 0.02 | 0.03 | 0.13 | 0.00 | 0.51 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.00 | 0.05 | 0.07 | 0.45 | 0.15 | 0.05 | 0.02 | 0.07 | 0.05 | 0.05 | 0.08 | 0.10 | 0.03 | 0.06 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.12 | 0.04 | 0.04 |
| PROZ | ENSG00000126231 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.21 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.12 | 0.07 | 0.23 | 0.05 | 0.15 | 0.01 | 0.22 | 0.03 | 0.15 | 0.03 | 0.10 | 0.01 | 0.17 | 0.02 | 0.02 | 0.02 | 0.29 | 0.00 | 0.06 | 0.04 | 0.13 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.16 | 0.05 | 0.26 | 0.14 | 0.23 | 0.01 | 0.09 | 0.03 | 0.33 | 0.12 | 0.45 | 0.10 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.12 | 0.04 | 0.03 | 0.05 | 0.02 | 0.08 | 0.00 | 0.07 | 0.07 |
| SLURP1 | ENSG00000126233 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.04 | 0.02 | 0.20 | 0.02 | 0.02 | 0.00 | 0.10 | 0.04 | 0.26 | 0.01 | 0.36 | 0.02 | 0.29 | 0.00 | 0.41 | 0.02 | 0.21 | 0.02 | 0.15 | 0.03 | 0.24 | 0.03 | 0.15 | 0.01 | 0.35 | 0.02 | 0.25 | 0.01 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.42 | 0.05 | 1.46 | 0.05 | 0.21 | 0.01 | 0.11 | 0.02 | 0.14 | 0.03 | 0.21 | 0.06 | 0.05 | 0.03 | 0.02 | 0.00 | 0.26 | 0.01 | 0.17 | 0.03 | 0.04 | 0.03 | 0.50 | 0.00 | 0.24 | 0.02 |
| GPR42 | ENSG00000126251 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.19 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 | 0.24 | 0.00 | 0.45 | 0.02 | 0.08 | 0.01 | 0.22 | 0.03 | 0.09 | 0.04 | 0.05 | 0.00 | 0.04 | 0.01 | 0.11 | 0.00 | 0.05 | 0.02 | 0.13 | 0.01 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.14 | 0.02 | 0.65 | 0.05 | 0.21 | 0.01 | 0.18 | 0.02 | 1.44 | 0.01 | 0.29 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.06 | 0.01 |
| FFAR2 | ENSG00000126262 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.19 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.25 | 0.00 | 0.44 | 0.03 | 0.08 | 0.01 | 0.22 | 0.03 | 0.08 | 0.04 | 0.05 | 0.00 | 0.04 | 0.01 | 0.11 | 0.00 | 0.05 | 0.02 | 0.13 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.14 | 0.02 | 0.64 | 0.05 | 0.22 | 0.01 | 0.18 | 0.02 | 1.50 | 0.01 | 0.31 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.02 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.05 | 0.01 |
| FFAR1 | ENSG00000126266 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.19 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 | 0.24 | 0.00 | 0.45 | 0.02 | 0.08 | 0.01 | 0.22 | 0.03 | 0.09 | 0.04 | 0.05 | 0.00 | 0.04 | 0.01 | 0.11 | 0.00 | 0.05 | 0.02 | 0.13 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.14 | 0.02 | 0.65 | 0.05 | 0.21 | 0.01 | 0.18 | 0.01 | 1.44 | 0.01 | 0.29 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.06 | 0.01 |
| STATH | ENSG00000126549 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.07 | 0.03 | 0.21 | 0.01 | 0.08 | 0.02 | 0.13 | 0.02 | 0.05 | 0.03 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.03 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.10 | 0.02 | 0.24 | 0.09 | 0.04 | 0.04 | 0.04 | 0.01 | 0.06 | 0.05 | 0.05 | 0.05 | 0.08 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| HTN1 | ENSG00000126550 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.08 | 0.03 | 0.21 | 0.01 | 0.08 | 0.02 | 0.12 | 0.02 | 0.05 | 0.03 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.03 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.10 | 0.02 | 0.24 | 0.08 | 0.04 | 0.04 | 0.04 | 0.01 | 0.06 | 0.05 | 0.05 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| WNK4 | ENSG00000126562 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.04 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.06 | 0.01 | 0.03 | 0.05 | 0.02 | 0.01 | 0.10 | 0.02 | 0.11 | 0.03 | 0.04 | 0.01 | 0.03 | 0.03 | 0.03 | 0.03 | 0.04 | 0.03 | 0.02 | 0.01 | 0.01 | 0.14 | 0.01 | 0.11 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.15 | 0.02 | 0.03 | 0.03 | 0.08 | 0.00 | 0.19 | 0.04 | 0.10 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.02 | 0.03 |
| CFP | ENSG00000126759 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.05 | 0.02 | 0.03 | 0.02 | 0.04 | 0.03 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.16 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.36 | 0.06 | 0.03 | 0.03 | 0.13 | 0.01 | 0.34 | 0.00 | 0.12 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 |
| PRDM7 | ENSG00000126856 | 0.00 | 0.00 | 0.01 | 0.04 | 0.00 | 0.06 | 0.01 | 0.23 | 0.08 | 0.06 | 0.00 | 0.00 | 0.02 | 0.19 | 0.01 | 0.12 | 0.04 | 0.07 | 0.03 | 0.05 | 0.08 | 0.05 | 0.05 | 0.05 | 0.02 | 0.03 | 0.03 | 0.04 | 0.02 | 0.01 | 0.02 | 0.08 | 0.05 | 0.05 | 0.07 | 0.06 | 0.00 | 0.02 | 0.00 | 0.01 | 0.05 | 0.10 | 0.08 | 0.35 | 0.05 | 0.07 | 0.01 | 0.09 | 0.03 | 0.29 | 0.09 | 0.07 | 0.00 | 0.12 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.06 | 0.02 | 0.11 |
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