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 |
| PSMB11 | ENSG00000222028 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.13 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.02 | 0.14 | 0.07 | 0.07 | 0.07 | 0.12 | 0.06 | 0.06 | 0.04 | 0.02 | 0.02 | 0.01 | 0.07 | 0.01 | 0.03 | 0.08 | 0.00 | 0.00 | 0.02 | 0.29 | 0.05 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 0.03 | 0.28 | 0.12 | 0.08 | 0.03 | 0.06 | 0.03 | 0.10 | 0.07 | 0.18 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.02 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| HLA-DPB1 | ENSG00000223865 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.01 | 0.04 | 0.05 | 0.02 | 0.04 | 0.13 | 0.04 | 0.08 | 0.04 | 0.03 | 0.02 | 0.08 | 0.02 | 0.03 | 0.01 | 0.07 | 0.01 | 0.05 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.27 | 0.06 | 0.09 | 0.01 | 0.05 | 0.01 | 0.05 | 0.01 | 0.05 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.10 | 0.01 | 0.00 | 0.01 | 0.01 | 0.11 | 0.00 | 0.11 | 0.01 |
| C1QTNF5 | ENSG00000223953 | 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 | 0.02 | 0.09 | 0.00 | 0.17 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.22 | 0.16 | 0.14 | 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 |
| C4B | ENSG00000224389 | 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 |
| HSP90AA2P | ENSG00000224411 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.05 | 0.03 | 0.02 | 0.03 | 0.09 | 0.02 | 0.05 | 0.02 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.06 | 0.03 | 0.11 | 0.11 | 0.00 | 0.03 | 0.03 | 0.02 | 0.11 | 0.10 | 0.05 | 0.08 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 |
| GPX5 | ENSG00000224586 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.16 | 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 | 0.07 | 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 | 0.05 | 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 |
| OR6V1 | ENSG00000225781 | 0.02 | 0.01 | 0.05 | 0.00 | 0.05 | 0.02 | 0.02 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.08 | 0.02 | 0.08 | 0.06 | 0.02 | 0.15 | 0.04 | 0.20 | 0.03 | 0.09 | 0.02 | 0.01 | 0.01 | 0.03 | 0.03 | 0.04 | 0.04 | 0.05 | 0.00 | 0.11 | 0.06 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.04 | 0.53 | 0.04 | 0.03 | 0.09 | 0.04 | 0.05 | 0.05 | 0.14 | 0.12 | 0.10 | 0.02 | 0.04 | 0.00 | 0.05 | 0.02 | 0.09 | 0.11 | 0.01 | 0.04 | 0.02 | 0.00 | 0.03 | 0.22 | 0.02 |
| OR52I2 | ENSG00000226288 | 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 |
| NPY6R | ENSG00000226306 | 0.28 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.02 | 0.03 | 0.01 | 0.03 | 0.03 | 0.03 | 0.02 | 0.06 | 0.01 | 0.03 | 0.02 | 0.02 | 0.01 | 0.01 | 0.08 | 0.02 | 0.09 | 0.01 | 0.24 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.03 | 0.02 | 0.12 | 0.12 | 0.03 | 0.02 | 0.02 | 0.01 | 0.10 | 0.01 | 0.09 | 0.04 | 0.00 | 0.00 | 0.00 | 0.10 | 0.04 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.03 | 0.03 | 0.11 |
| TAS2R46 | ENSG00000226761 | 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 | 0.12 | 0.01 | 0.10 | 0.03 | 0.05 | 0.04 | 0.03 | 0.08 | 0.01 | 0.03 | 0.03 | 0.03 | 0.01 | 0.06 | 0.00 | 0.06 | 0.14 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.06 | 0.33 | 0.10 | 0.01 | 0.02 | 0.03 | 0.03 | 0.04 | 0.03 | 0.12 | 0.16 | 0.55 | 0.00 | 0.00 | 0.03 | 0.00 | 0.04 | 0.09 | 0.01 | 0.01 | 0.05 | 0.00 | 0.01 | 0.04 | 0.03 |
| LTA | ENSG00000226979 | 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 |
| LTB | ENSG00000227507 | 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 |
| IFNA14 | ENSG00000228083 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.06 | 0.01 | 0.04 | 0.09 | 0.42 | 0.00 | 0.04 | 0.00 | 0.77 | 0.03 | 0.27 | 0.05 | 0.36 | 0.06 | 0.17 | 0.02 | 0.29 | 0.01 | 0.21 | 0.02 | 0.02 | 0.01 | 0.02 | 0.03 | 0.36 | 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 | 0.23 | 0.01 | 1.83 | 0.00 | 0.00 | 0.01 | 0.32 |
| OR2M3 | ENSG00000228198 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.04 | 0.14 | 0.04 | 0.02 | 0.02 | 0.08 | 0.05 | 0.13 | 0.01 | 0.17 | 0.03 | 0.10 | 0.02 | 0.27 | 0.04 | 0.13 | 0.01 | 0.04 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.20 | 0.02 | 0.23 | 0.02 | 0.10 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.29 | 0.02 | 0.48 | 0.12 | 0.13 | 0.01 | 0.12 | 0.02 | 0.32 | 0.00 | 0.09 | 0.24 | 0.06 | 0.02 | 0.01 | 0.00 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.24 | 0.02 |
| MT-ATP8 | ENSG00000228253 | 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 |
| VN1R4 | ENSG00000228567 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.19 | 0.03 | 0.00 | 0.00 | 0.01 | 0.06 | 0.02 | 0.06 | 0.07 | 0.09 | 0.02 | 0.02 | 0.09 | 0.03 | 0.09 | 0.03 | 0.02 | 0.03 | 0.01 | 0.04 | 0.03 | 0.04 | 0.05 | 0.03 | 0.00 | 0.07 | 0.22 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.14 | 0.03 | 0.12 | 0.27 | 0.10 | 0.05 | 0.06 | 0.05 | 0.45 | 0.10 | 0.07 | 0.17 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.06 | 0.01 | 0.17 | 0.02 | 0.13 | 0.00 | 0.00 | 0.04 | 0.03 |
| DHFR | ENSG00000228716 | 0.01 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.00 | 0.13 | 0.01 | 0.11 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.07 | 0.00 | 0.09 | 0.01 | 0.08 | 0.02 | 0.14 | 0.01 | 0.12 | 0.01 | 0.06 | 0.01 | 0.04 | 0.00 | 0.07 | 0.01 | 0.04 | 0.00 | 0.08 | 0.10 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.09 | 0.03 | 0.67 | 0.00 | 0.05 | 0.01 | 0.09 | 0.06 | 0.21 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 |
| PGA4 | ENSG00000229183 | 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 | 0.06 | 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 | 0.15 | 0.06 | 0.13 | 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 |
| ORM1 | ENSG00000229314 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.02 | 0.04 | 0.01 | 0.05 | 0.00 | 0.13 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.03 | 0.06 | 0.06 | 0.04 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.11 | 0.11 | 0.04 | 0.00 | 0.01 | 0.04 | 0.00 | 0.15 | 0.07 | 0.04 | 0.03 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 |
| SPINK8 | ENSG00000229453 | 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 | 0.08 | 0.00 | 0.09 | 0.00 | 0.06 | 0.01 | 0.11 | 0.01 | 0.11 | 0.00 | 0.05 | 0.02 | 0.10 | 0.00 | 0.04 | 0.02 | 0.05 | 0.00 | 0.24 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.16 | 0.10 | 0.18 | 0.00 | 0.06 | 0.07 | 0.04 | 0.05 | 0.32 | 0.03 | 0.14 | 0.02 | 0.04 | 0.00 | 0.01 | 0.00 | 0.09 | 0.01 | 0.05 | 0.02 | 0.04 | 0.00 | 0.03 | 0.02 | 0.05 |
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