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 |
| PGA3 | ENSG00000229859 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.01 | 0.00 | 0.11 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 | 0.07 | 0.01 | 0.06 | 0.02 | 0.12 | 0.02 | 0.13 | 0.02 | 0.05 | 0.03 | 0.01 | 0.02 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.02 | 0.11 | 0.12 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.14 | 0.06 | 0.12 | 0.05 | 0.05 | 0.01 | 0.04 | 0.02 | 0.17 | 0.14 | 0.05 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.04 |
| PRPS1L1 | ENSG00000229937 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.25 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.11 | 0.00 | 0.10 | 0.01 | 0.06 | 0.01 | 0.17 | 0.02 | 0.08 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.15 | 0.27 | 0.01 | 0.01 | 0.07 | 0.04 | 0.04 | 0.03 | 0.13 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.03 | 0.06 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 |
| OR5H6 | ENSG00000230301 | 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 | 0.18 | 0.03 | 0.06 | 0.01 | 0.11 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.12 | 0.10 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.21 | 0.04 | 0.05 | 0.02 | 0.04 | 0.00 | 0.18 | 0.08 | 0.07 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| OR5H1 | ENSG00000231192 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.01 | 0.20 | 0.03 | 0.07 | 0.01 | 0.11 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 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 | 0.08 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| SBK3 | ENSG00000231274 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.21 | 0.03 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.06 | 0.12 | 0.08 | 0.06 | 0.02 | 0.12 | 0.03 | 0.12 | 0.02 | 0.02 | 0.03 | 0.01 | 0.04 | 0.05 | 0.04 | 0.06 | 0.02 | 0.02 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.18 | 0.03 | 0.16 | 0.28 | 0.14 | 0.05 | 0.07 | 0.05 | 0.37 | 0.10 | 0.05 | 0.18 | 0.00 | 0.06 | 0.01 | 0.00 | 0.26 | 0.03 | 0.01 | 0.19 | 0.03 | 0.12 | 0.00 | 0.00 | 0.03 | 0.05 |
| CYP21A2 | ENSG00000231852 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.13 | 0.05 | 0.12 | 0.04 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.29 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.12 | 0.01 |
| OR5K2 | ENSG00000231861 | 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 | 0.23 | 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 |
| PRH1 | ENSG00000231887 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.16 | 0.04 | 0.08 | 0.01 | 0.00 | 0.00 | 0.05 | 0.04 | 0.10 | 0.14 | 0.01 | 0.10 | 0.03 | 0.05 | 0.04 | 0.04 | 0.08 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.07 | 0.01 | 0.06 | 0.14 | 0.05 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.10 | 0.06 | 0.34 | 0.10 | 0.03 | 0.02 | 0.03 | 0.03 | 0.04 | 0.03 | 0.17 | 0.16 | 0.55 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.10 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.04 | 0.03 |
| OR2H5P | ENSG00000232173 | 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 | 0.07 | 0.02 | 0.06 | 0.05 | 0.02 | 0.04 | 0.16 | 0.08 | 0.10 | 0.04 | 0.04 | 0.02 | 0.06 | 0.01 | 0.04 | 0.02 | 0.09 | 0.01 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.02 | 0.32 | 0.06 | 0.09 | 0.04 | 0.03 | 0.01 | 0.17 | 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 |
| MTRNR2L4 | ENSG00000232196 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.18 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.03 | 0.03 | 0.09 | 0.04 | 0.02 | 0.02 | 0.08 | 0.02 | 0.08 | 0.03 | 0.03 | 0.03 | 0.03 | 0.02 | 0.02 | 0.03 | 0.02 | 0.05 | 0.05 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.08 | 0.23 | 0.10 | 0.02 | 0.02 | 0.07 | 0.02 | 0.05 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 |
| OR52I1 | ENSG00000232268 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.10 | 0.00 | 0.00 | 0.03 | 0.05 | 0.02 | 0.06 | 0.02 | 0.14 | 0.01 | 0.07 | 0.02 | 0.10 | 0.03 | 0.05 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.04 | 0.03 | 0.03 | 0.01 | 0.01 | 0.07 | 0.03 | 0.07 | 0.00 | 0.00 | 0.02 | 0.11 | 0.02 | 0.44 | 0.01 | 0.05 | 0.02 | 0.06 | 0.03 | 0.09 | 0.05 | 0.14 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.10 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 |
| OR5K1 | ENSG00000232382 | 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 | 0.23 | 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 |
| TNF | ENSG00000232810 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.15 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.06 | 0.05 | 0.03 | 0.04 | 0.13 | 0.05 | 0.12 | 0.04 | 0.03 | 0.02 | 0.07 | 0.02 | 0.05 | 0.01 | 0.11 | 0.01 | 0.05 | 0.03 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.29 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.10 | 0.03 | 0.06 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.01 | 0.11 | 0.00 | 0.12 | 0.01 |
| GPX1 | ENSG00000233276 | 0.00 | 0.18 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 | 0.15 | 0.00 | 0.01 | 0.00 | 0.54 | 0.01 | 0.06 | 0.00 | 0.10 | 0.00 | 0.06 | 0.01 | 0.13 | 0.01 | 0.11 | 0.00 | 0.06 | 0.02 | 0.09 | 0.00 | 0.04 | 0.04 | 0.05 | 0.00 | 0.24 | 0.05 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.07 | 0.19 | 0.00 | 0.06 | 0.06 | 0.06 | 0.04 | 0.30 | 0.03 | 0.16 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.16 | 0.00 | 0.05 | 0.02 | 0.04 | 0.00 | 0.03 | 0.01 | 0.04 |
| OR5H15 | ENSG00000233412 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.01 | 0.19 | 0.03 | 0.07 | 0.01 | 0.11 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 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 | 0.21 | 0.04 | 0.05 | 0.01 | 0.04 | 0.00 | 0.18 | 0.08 | 0.08 | 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 |
| OR10G8 | ENSG00000234560 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.02 | 0.02 | 0.06 | 0.03 | 0.09 | 0.00 | 0.00 | 0.13 | 0.06 | 0.05 | 0.09 | 0.05 | 0.10 | 0.04 | 0.14 | 0.05 | 0.15 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.09 | 0.00 | 0.19 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.22 | 0.19 | 0.17 | 0.04 | 0.31 | 0.04 | 0.07 | 0.05 | 0.17 | 0.05 | 0.24 | 0.00 | 0.24 | 0.03 | 0.00 | 0.13 | 0.02 | 0.06 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.01 | 0.26 |
| IFNA17 | ENSG00000234829 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.06 | 0.01 | 0.03 | 0.09 | 0.41 | 0.00 | 0.04 | 0.00 | 0.76 | 0.03 | 0.27 | 0.05 | 0.36 | 0.06 | 0.16 | 0.02 | 0.29 | 0.01 | 0.21 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.37 | 0.01 | 0.10 | 0.00 | 0.16 | 0.00 | 0.13 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.09 | 0.07 | 0.18 | 0.06 | 0.05 | 0.05 | 0.02 | 0.04 | 0.05 | 0.05 | 0.26 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.24 | 0.01 | 1.02 | 0.00 | 0.00 | 0.01 | 0.32 |
| APOC2 | ENSG00000234906 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.14 | 0.02 | 0.00 | 0.00 | 0.03 | 0.05 | 0.12 | 0.05 | 0.11 | 0.08 | 0.06 | 0.02 | 0.06 | 0.05 | 0.12 | 0.01 | 0.01 | 0.02 | 0.01 | 0.02 | 0.09 | 0.02 | 0.06 | 0.04 | 0.12 | 0.03 | 0.25 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.05 | 0.16 | 0.30 | 0.20 | 0.03 | 0.13 | 0.04 | 0.30 | 0.17 | 0.07 | 0.17 | 0.00 | 0.04 | 0.01 | 0.00 | 0.07 | 0.03 | 0.02 | 0.13 | 0.02 | 0.09 | 0.00 | 0.00 | 0.02 | 0.02 |
| KDM4E | ENSG00000235268 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.04 | 0.02 | 0.09 | 0.05 | 0.00 | 0.00 | 0.06 | 0.06 | 0.08 | 0.04 | 0.07 | 0.09 | 0.07 | 0.10 | 0.10 | 0.07 | 0.05 | 0.04 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.10 | 0.13 | 0.31 | 0.10 | 0.18 | 0.08 | 0.06 | 0.03 | 0.13 | 0.16 | 0.05 | 0.13 | 0.04 | 0.07 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.10 |
| OR5H14 | ENSG00000236032 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.01 | 0.20 | 0.03 | 0.07 | 0.01 | 0.11 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.12 | 0.10 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.21 | 0.04 | 0.05 | 0.01 | 0.04 | 0.00 | 0.18 | 0.08 | 0.08 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
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