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 |
| ABL2 | ENSG00000143322 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.23 | 0.02 | 0.02 | 0.00 | 0.09 | 0.03 | 0.11 | 0.00 | 0.18 | 0.01 | 0.03 | 0.00 | 0.17 | 0.03 | 0.10 | 0.01 | 0.03 | 0.00 | 0.13 | 0.00 | 0.04 | 0.00 | 0.17 | 0.01 | 0.20 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 | 0.36 | 0.03 | 0.08 | 0.01 | 0.09 | 0.01 | 0.25 | 0.00 | 0.28 | 0.03 | 0.08 | 0.00 | 0.00 | 0.00 | 0.32 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.10 | 0.03 |
| MTF2 | ENSG00000143033 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.39 | 0.04 | 0.10 | 0.04 | 0.06 | 0.01 | 0.07 | 0.01 | 0.08 | 0.02 | 0.08 | 0.00 | 0.06 | 0.01 | 0.05 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.16 | 0.02 | 0.05 | 0.00 | 0.23 | 0.00 | 0.00 | 0.06 | 0.11 | 0.15 | 0.17 | 0.00 | 0.05 | 0.02 | 0.03 | 0.05 | 0.06 | 0.09 | 0.09 | 0.03 | 0.06 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.01 | 0.08 | 0.00 | 0.05 | 0.03 | 0.13 |
| ABCC5 | ENSG00000114770 | 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 |
| PEBP4 | ENSG00000134020 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.24 | 0.00 | 0.15 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.11 | 0.00 | 0.07 | 0.02 | 0.07 | 0.04 | 0.05 | 0.00 | 0.12 | 0.01 | 0.17 | 0.00 | 0.06 | 0.00 | 0.13 | 0.00 | 0.05 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.01 | 0.45 | 0.01 | 0.06 | 0.01 | 0.11 | 0.00 | 0.24 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 | 0.05 |
| ADAMTS9 | ENSG00000163638 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.04 | 0.04 | 0.16 | 0.00 | 0.04 | 0.01 | 0.21 | 0.03 | 0.03 | 0.01 | 0.11 | 0.01 | 0.06 | 0.05 | 0.11 | 0.05 | 0.05 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.02 | 0.07 | 0.00 | 0.17 | 0.08 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.11 | 0.14 | 0.00 | 0.13 | 0.03 | 0.07 | 0.20 | 0.26 | 0.03 | 0.13 | 0.08 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.03 | 0.00 | 0.03 | 0.00 | 0.03 | 0.07 | 0.01 |
| NOS2 | ENSG00000007171 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.21 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.08 | 0.01 | 0.14 | 0.02 | 0.05 | 0.02 | 0.19 | 0.03 | 0.14 | 0.02 | 0.11 | 0.02 | 0.08 | 0.00 | 0.03 | 0.01 | 0.04 | 0.00 | 0.07 | 0.01 | 0.02 | 0.05 | 0.00 | 0.13 | 0.00 | 0.00 | 0.27 | 0.03 | 0.11 | 0.07 | 0.00 | 0.03 | 0.09 | 0.04 | 0.11 | 0.06 | 0.08 | 0.12 | 0.00 | 0.01 | 0.00 | 0.02 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.04 |
| STRADA | ENSG00000266173 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.25 | 0.00 | 0.02 | 0.00 | 0.12 | 0.00 | 0.14 | 0.01 | 0.19 | 0.01 | 0.07 | 0.02 | 0.25 | 0.03 | 0.12 | 0.02 | 0.08 | 0.01 | 0.08 | 0.02 | 0.08 | 0.10 | 0.19 | 0.00 | 0.12 | 0.01 | 0.19 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.56 | 0.01 | 0.25 | 0.03 | 0.19 | 0.03 | 0.11 | 0.03 | 0.27 | 0.02 | 0.17 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.06 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.24 | 0.01 |
| RPS6KB1 | ENSG00000108443 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.24 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.16 | 0.01 | 0.16 | 0.02 | 0.05 | 0.01 | 0.20 | 0.03 | 0.14 | 0.01 | 0.08 | 0.01 | 0.10 | 0.03 | 0.04 | 0.12 | 0.24 | 0.00 | 0.12 | 0.01 | 0.08 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.71 | 0.01 | 0.25 | 0.02 | 0.11 | 0.02 | 0.13 | 0.03 | 0.59 | 0.00 | 0.19 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.03 | 0.01 | 0.16 | 0.00 | 0.22 | 0.01 |
| SLC38A5 | ENSG00000017483 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.05 | 0.02 | 0.02 | 0.02 | 0.04 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.17 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.43 | 0.07 | 0.03 | 0.03 | 0.11 | 0.01 | 0.19 | 0.03 | 0.11 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| NAALADL1 | ENSG00000168060 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.07 | 0.03 | 0.07 | 0.02 | 0.19 | 0.02 | 0.15 | 0.04 | 0.04 | 0.03 | 0.01 | 0.02 | 0.04 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 | 0.00 | 0.11 | 0.07 | 0.07 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.09 | 0.19 | 0.04 | 0.10 | 0.01 | 0.09 | 0.03 | 0.22 | 0.06 | 0.09 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.06 |
| SEMA3C | ENSG00000075223 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.01 | 0.11 | 0.02 | 0.09 | 0.02 | 0.20 | 0.02 | 0.09 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.04 | 0.01 | 0.03 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.13 | 0.08 | 0.04 | 0.01 | 0.02 | 0.02 | 0.12 | 0.03 | 0.08 | 0.05 | 0.08 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 |
| F5 | ENSG00000198734 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.45 | 0.01 | 0.02 | 0.02 | 0.10 | 0.03 | 0.13 | 0.01 | 0.24 | 0.01 | 0.04 | 0.00 | 0.22 | 0.01 | 0.12 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.23 | 0.00 | 0.22 | 0.05 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.20 | 0.02 | 0.33 | 0.02 | 0.11 | 0.01 | 0.10 | 0.00 | 0.29 | 0.00 | 0.46 | 0.04 | 0.10 | 0.00 | 0.00 | 0.00 | 0.36 | 0.04 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.14 | 0.01 |
| SLC6A9 | ENSG00000196517 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.12 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.10 | 0.02 | 0.10 | 0.02 | 0.08 | 0.01 | 0.08 | 0.03 | 0.05 | 0.03 | 0.02 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.08 | 0.00 | 0.27 | 0.01 | 0.03 | 0.02 | 0.11 | 0.00 | 0.00 | 0.08 | 0.04 | 0.47 | 0.05 | 0.11 | 0.00 | 0.09 | 0.01 | 0.18 | 0.03 | 0.11 | 0.03 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.05 | 0.02 |
| KDM6A | ENSG00000147050 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.01 | 0.04 | 0.10 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.03 | 0.06 | 0.10 | 0.02 | 0.08 | 0.09 | 0.25 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.15 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.17 | 0.11 | 0.02 | 0.09 | 0.07 | 0.03 | 0.29 | 0.05 | 0.11 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| KALRN | ENSG00000160145 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.04 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.02 | 0.14 | 0.01 | 0.05 | 0.00 | 0.10 | 0.05 | 0.05 | 0.02 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.00 | 0.05 | 0.03 | 0.03 | 0.01 | 0.07 | 0.00 | 0.00 | 0.04 | 0.04 | 0.25 | 0.04 | 0.08 | 0.01 | 0.08 | 0.01 | 0.15 | 0.07 | 0.13 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.03 | 0.01 | 0.06 | 0.00 | 0.00 | 0.02 | 0.04 |
| PLXNB1 | ENSG00000164050 | 0.00 | 0.18 | 0.00 | 0.02 | 0.05 | 0.00 | 0.00 | 0.03 | 0.03 | 0.14 | 0.00 | 0.04 | 0.00 | 0.55 | 0.01 | 0.07 | 0.00 | 0.09 | 0.00 | 0.06 | 0.02 | 0.11 | 0.01 | 0.11 | 0.00 | 0.05 | 0.02 | 0.10 | 0.00 | 0.04 | 0.03 | 0.05 | 0.00 | 0.24 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.16 | 0.08 | 0.19 | 0.00 | 0.06 | 0.06 | 0.05 | 0.05 | 0.32 | 0.03 | 0.13 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.09 | 0.01 | 0.06 | 0.02 | 0.04 | 0.00 | 0.03 | 0.02 | 0.05 |
| ALDH1A1 | ENSG00000165092 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.00 | 0.01 | 0.02 | 0.06 | 0.00 | 0.06 | 0.06 | 0.06 | 0.01 | 0.03 | 0.10 | 0.03 | 0.06 | 0.05 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.15 | 0.05 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.04 | 0.12 | 0.15 | 0.01 | 0.03 | 0.04 | 0.03 | 0.00 | 0.16 | 0.12 | 0.01 | 0.02 | 0.03 | 0.00 | 0.02 | 0.05 | 0.03 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.02 | 0.03 |
| ABCA7 | ENSG00000064687 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.15 | 0.05 | 0.00 | 0.03 | 0.10 | 0.04 | 0.09 | 0.02 | 0.15 | 0.01 | 0.15 | 0.04 | 0.18 | 0.04 | 0.08 | 0.01 | 0.07 | 0.02 | 0.09 | 0.01 | 0.07 | 0.02 | 0.14 | 0.04 | 0.03 | 0.19 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.17 | 0.03 | 0.91 | 0.05 | 0.24 | 0.03 | 0.26 | 0.00 | 0.78 | 0.23 | 0.20 | 0.01 | 0.01 | 0.00 | 0.02 | 0.07 | 0.00 | 0.06 | 0.02 | 0.07 | 0.01 | 0.01 | 0.02 | 0.03 | 0.08 |
| GDF6 | ENSG00000156466 | 0.00 | 0.00 | 0.01 | 0.00 | 0.14 | 0.00 | 0.08 | 0.02 | 0.29 | 0.00 | 0.02 | 0.00 | 0.02 | 0.03 | 0.17 | 0.01 | 0.18 | 0.01 | 0.10 | 0.00 | 0.21 | 0.01 | 0.14 | 0.01 | 0.08 | 0.01 | 0.18 | 0.02 | 0.04 | 0.01 | 0.25 | 0.01 | 0.19 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.38 | 0.00 | 0.51 | 0.07 | 0.10 | 0.00 | 0.10 | 0.01 | 0.38 | 0.02 | 0.18 | 0.03 | 0.15 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.12 | 0.00 | 0.01 | 0.00 | 0.39 | 0.00 | 0.12 | 0.01 |
| PDE10A | ENSG00000112541 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.05 | 0.03 | 0.11 | 0.00 | 0.01 | 0.00 | 0.09 | 0.02 | 0.06 | 0.08 | 0.07 | 0.04 | 0.04 | 0.11 | 0.04 | 0.09 | 0.08 | 0.02 | 0.02 | 0.03 | 0.04 | 0.01 | 0.04 | 0.02 | 0.13 | 0.00 | 0.18 | 0.20 | 0.10 | 0.00 | 0.03 | 0.01 | 0.00 | 0.08 | 0.13 | 0.07 | 0.44 | 0.00 | 0.10 | 0.04 | 0.05 | 0.21 | 0.06 | 0.23 | 0.07 | 0.01 | 0.05 | 0.00 | 0.00 | 0.03 | 0.04 | 0.00 | 0.05 | 0.01 | 0.17 | 0.05 | 0.06 | 0.04 | 0.15 |
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