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 |
| PSMA8 | ENSG00000154611 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.03 | 0.00 | 0.00 | 0.03 | 0.03 | 0.12 | 0.02 | 0.24 | 0.03 | 0.17 | 0.04 | 0.19 | 0.05 | 0.11 | 0.05 | 0.03 | 0.03 | 0.02 | 0.07 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.01 | 0.33 | 0.04 | 0.03 | 0.02 | 0.12 | 0.00 | 0.05 | 0.03 | 0.07 | 0.05 | 0.00 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| GPX6 | ENSG00000198704 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.17 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 | 0.07 | 0.02 | 0.06 | 0.06 | 0.03 | 0.04 | 0.13 | 0.08 | 0.08 | 0.05 | 0.04 | 0.02 | 0.06 | 0.01 | 0.02 | 0.03 | 0.10 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.31 | 0.06 | 0.10 | 0.03 | 0.05 | 0.01 | 0.26 | 0.02 | 0.08 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.14 | 0.01 |
| OR2H1 | ENSG00000204688 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.15 | 0.08 | 0.09 | 0.04 | 0.04 | 0.02 | 0.06 | 0.01 | 0.04 | 0.02 | 0.10 | 0.01 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.31 | 0.05 | 0.09 | 0.03 | 0.03 | 0.01 | 0.26 | 0.02 | 0.03 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.13 | 0.01 |
| UGT1A3 | ENSG00000243135 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.33 | 0.00 | 0.04 | 0.00 | 0.08 | 0.03 | 0.05 | 0.02 | 0.20 | 0.01 | 0.19 | 0.05 | 0.16 | 0.03 | 0.08 | 0.02 | 0.03 | 0.02 | 0.02 | 0.04 | 0.03 | 0.03 | 0.06 | 0.00 | 0.01 | 0.00 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.10 | 0.17 | 0.23 | 0.01 | 0.39 | 0.03 | 0.06 | 0.13 | 0.06 | 0.04 | 0.40 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.05 | 0.01 | 0.08 | 0.01 | 0.12 |
| PCDHA2 | ENSG00000204969 | 0.30 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.04 | 0.02 | 0.01 | 0.05 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.08 | 0.02 | 0.09 | 0.01 | 0.24 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.04 | 0.02 | 0.15 | 0.11 | 0.03 | 0.01 | 0.02 | 0.02 | 0.14 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.14 |
| TMPRSS12 | ENSG00000186452 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.11 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.09 | 0.04 | 0.04 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.04 | 0.03 | 0.01 | 0.09 | 0.05 | 0.21 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.05 | 0.11 | 0.05 | 0.04 | 0.00 | 0.05 | 0.01 | 0.29 | 0.04 | 0.13 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.03 | 0.03 | 0.02 | 0.05 | 0.00 | 0.00 | 0.04 | 0.07 |
| MCHR2 | ENSG00000152034 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.33 | 0.01 | 0.10 | 0.00 | 0.01 | 0.00 | 0.08 | 0.01 | 0.05 | 0.03 | 0.04 | 0.02 | 0.03 | 0.04 | 0.10 | 0.04 | 0.08 | 0.00 | 0.03 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.07 | 0.00 | 0.11 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.10 | 0.15 | 0.16 | 0.03 | 0.01 | 0.04 | 0.02 | 0.06 | 0.04 | 0.12 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.30 | 0.00 | 0.01 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.08 |
| TEX101 | ENSG00000131126 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.07 | 0.14 | 0.03 | 0.00 | 0.00 | 0.05 | 0.07 | 0.11 | 0.05 | 0.13 | 0.08 | 0.02 | 0.02 | 0.06 | 0.07 | 0.07 | 0.02 | 0.02 | 0.02 | 0.02 | 0.03 | 0.07 | 0.03 | 0.04 | 0.03 | 0.12 | 0.01 | 0.14 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.05 | 0.20 | 0.28 | 0.17 | 0.05 | 0.05 | 0.05 | 0.09 | 0.17 | 0.11 | 0.12 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.03 | 0.01 | 0.12 | 0.03 | 0.09 | 0.00 | 0.00 | 0.02 | 0.03 |
| PDILT | ENSG00000169340 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.01 | 0.04 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.03 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.13 | 0.04 | 0.05 | 0.00 | 0.07 | 0.01 | 0.09 | 0.00 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 |
| SLC9C2 | ENSG00000162753 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.34 | 0.01 | 0.02 | 0.00 | 0.10 | 0.03 | 0.13 | 0.00 | 0.22 | 0.01 | 0.04 | 0.01 | 0.20 | 0.02 | 0.11 | 0.01 | 0.04 | 0.00 | 0.12 | 0.00 | 0.05 | 0.00 | 0.22 | 0.00 | 0.17 | 0.01 | 0.00 | 0.06 | 0.04 | 0.01 | 0.00 | 0.00 | 0.17 | 0.01 | 0.34 | 0.03 | 0.13 | 0.00 | 0.11 | 0.00 | 0.29 | 0.03 | 0.45 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.30 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.14 | 0.01 |
| HTR3D | ENSG00000186090 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.03 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.15 | 0.05 | 1.90 | 0.00 | 0.68 | 0.00 | 0.67 | 0.02 | 0.24 | 0.01 | 0.04 | 0.00 | 0.06 | 0.03 | 0.03 | 0.01 | 0.11 | 0.02 | 0.12 | 0.01 | 0.12 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.19 | 0.02 | 1.12 | 0.02 | 0.63 | 0.00 | 0.34 | 0.01 | 0.76 | 0.09 | 0.11 | 0.10 | 0.22 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.07 | 0.00 | 0.20 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 |
| USH2A | ENSG00000042781 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.07 | 0.07 | 0.07 | 0.02 | 0.00 | 0.07 | 0.06 | 0.08 | 0.01 | 0.10 | 0.01 | 0.05 | 0.00 | 0.17 | 0.04 | 0.06 | 0.02 | 0.04 | 0.01 | 0.05 | 0.05 | 0.00 | 0.01 | 0.14 | 0.02 | 0.16 | 0.02 | 0.04 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.22 | 0.02 | 0.20 | 0.16 | 0.06 | 0.01 | 0.05 | 0.03 | 0.15 | 0.04 | 0.02 | 0.22 | 0.02 | 0.03 | 0.01 | 0.00 | 0.13 | 0.06 | 0.00 | 0.02 | 0.03 | 0.06 | 0.09 | 0.00 | 0.13 | 0.03 |
| CHRNB3 | ENSG00000147432 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.07 | 0.21 | 0.05 | 0.00 | 0.00 | 0.04 | 0.00 | 0.17 | 0.04 | 0.35 | 0.03 | 0.11 | 0.03 | 0.38 | 0.07 | 0.09 | 0.03 | 0.16 | 0.02 | 0.10 | 0.05 | 0.03 | 0.00 | 0.03 | 0.04 | 0.00 | 0.02 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.35 | 0.05 | 0.30 | 0.03 | 0.08 | 0.03 | 0.18 | 0.01 | 0.96 | 0.10 | 0.12 | 0.06 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 |
| CHST5 | ENSG00000135702 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.21 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.10 | 0.05 | 0.05 | 0.06 | 0.04 | 0.03 | 0.02 | 0.06 | 0.04 | 0.04 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.05 | 0.05 | 0.01 | 0.05 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.06 | 0.29 | 0.04 | 0.02 | 0.03 | 0.08 | 0.01 | 0.19 | 0.03 | 0.05 | 0.01 | 0.08 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 |
| PTH | ENSG00000152266 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.03 | 0.09 | 0.00 | 0.00 | 0.02 | 0.00 | 0.07 | 0.04 | 0.11 | 0.09 | 0.05 | 0.04 | 0.06 | 0.04 | 0.03 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.04 | 0.07 | 0.06 | 0.31 | 0.01 | 0.04 | 0.08 | 0.04 | 0.17 | 0.04 | 0.11 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 |
| OPRM1 | ENSG00000112038 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.02 | 0.09 | 0.00 | 0.02 | 0.00 | 0.18 | 0.02 | 0.06 | 0.06 | 0.05 | 0.03 | 0.03 | 0.09 | 0.04 | 0.10 | 0.05 | 0.02 | 0.02 | 0.04 | 0.02 | 0.01 | 0.03 | 0.01 | 0.12 | 0.00 | 0.18 | 0.06 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.09 | 0.05 | 0.39 | 0.01 | 0.07 | 0.03 | 0.04 | 0.11 | 0.03 | 0.27 | 0.04 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.05 | 0.01 | 0.08 | 0.05 | 0.09 | 0.02 | 0.14 |
| CCNB3 | ENSG00000147082 | 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 |
| CDKL4 | ENSG00000205111 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.06 | 0.01 | 0.10 | 0.02 | 0.04 | 0.02 | 0.05 | 0.03 | 0.02 | 0.03 | 0.00 | 0.01 | 0.02 | 0.03 | 0.01 | 0.02 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.22 | 0.05 | 0.08 | 0.00 | 0.08 | 0.02 | 0.16 | 0.00 | 0.07 | 0.07 | 0.18 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.02 | 0.01 |
| PROL1 | ENSG00000171199 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.08 | 0.03 | 0.21 | 0.01 | 0.08 | 0.02 | 0.10 | 0.02 | 0.05 | 0.03 | 0.01 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.07 | 0.00 | 0.08 | 0.06 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.11 | 0.02 | 0.24 | 0.08 | 0.04 | 0.04 | 0.04 | 0.01 | 0.13 | 0.05 | 0.07 | 0.06 | 0.10 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| OR5V1 | ENSG00000243729 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.16 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.07 | 0.06 | 0.03 | 0.04 | 0.13 | 0.08 | 0.09 | 0.05 | 0.04 | 0.02 | 0.06 | 0.01 | 0.04 | 0.02 | 0.11 | 0.01 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.31 | 0.05 | 0.09 | 0.04 | 0.03 | 0.01 | 0.26 | 0.02 | 0.03 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.15 | 0.01 |
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