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 |
| OR10R3P | ENSG00000198703 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.42 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.28 | 0.00 | 0.25 | 0.00 | 0.06 | 0.01 | 0.25 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.29 | 0.00 | 0.41 | 0.01 | 0.18 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.38 | 0.02 | 0.15 | 0.00 | 0.14 | 0.00 | 0.29 | 0.00 | 0.37 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 |
| MT-CO2 | ENSG00000198712 | 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 |
| SLC5A3 | ENSG00000198743 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.02 | 0.04 | 0.04 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.03 | 0.02 | 0.01 | 0.04 | 0.01 | 0.01 | 0.01 | 0.00 | 0.05 | 0.03 | 0.12 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.10 | 0.06 | 0.02 | 0.03 | 0.03 | 0.01 | 0.03 | 0.03 | 0.06 | 0.07 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 |
| GRIN3A | ENSG00000198785 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.04 | 0.06 | 0.00 | 0.01 | 0.02 | 0.06 | 0.02 | 0.03 | 0.05 | 0.01 | 0.04 | 0.00 | 0.10 | 0.01 | 0.02 | 0.04 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.03 | 0.04 | 0.00 | 0.08 | 0.10 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.08 | 0.15 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.15 | 0.12 | 0.02 | 0.04 | 0.02 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 |
| MUC2 | ENSG00000198788 | 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 |
| PNP | ENSG00000198805 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.04 | 0.18 | 0.07 | 0.08 | 0.06 | 0.12 | 0.06 | 0.08 | 0.04 | 0.03 | 0.02 | 0.01 | 0.10 | 0.01 | 0.04 | 0.09 | 0.00 | 0.00 | 0.02 | 0.18 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.41 | 0.10 | 0.07 | 0.02 | 0.08 | 0.03 | 0.15 | 0.08 | 0.18 | 0.08 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| CES1 | ENSG00000198848 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.04 | 0.04 | 0.02 | 0.03 | 0.03 | 0.10 | 0.01 | 0.02 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.06 | 0.06 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.04 | 0.04 | 0.14 | 0.00 | 0.08 | 0.03 | 0.06 | 0.05 | 0.12 | 0.01 | 0.07 | 0.12 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.00 | 0.05 |
| CD3E | ENSG00000198851 | 0.02 | 0.01 | 0.00 | 0.06 | 0.02 | 0.02 | 0.02 | 0.08 | 0.04 | 0.10 | 0.00 | 0.02 | 0.07 | 0.04 | 0.05 | 0.07 | 0.05 | 0.09 | 0.05 | 0.16 | 0.04 | 0.12 | 0.07 | 0.07 | 0.01 | 0.01 | 0.03 | 0.03 | 0.01 | 0.02 | 0.02 | 0.09 | 0.00 | 0.17 | 0.03 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.04 | 0.23 | 0.14 | 0.14 | 0.04 | 0.30 | 0.05 | 0.05 | 0.15 | 0.16 | 0.04 | 0.21 | 0.00 | 0.15 | 0.02 | 0.00 | 0.14 | 0.01 | 0.08 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.01 | 0.25 |
| STKLD1 | ENSG00000198870 | 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 |
| OR5D13 | ENSG00000198877 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.01 | 0.03 | 0.13 | 0.04 | 0.00 | 0.01 | 0.04 | 0.03 | 0.04 | 0.03 | 0.08 | 0.03 | 0.11 | 0.01 | 0.16 | 0.05 | 0.01 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.05 | 0.07 | 0.07 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.12 | 0.06 | 0.04 | 0.02 | 0.04 | 0.03 | 0.34 | 0.03 | 0.10 | 0.05 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.05 | 0.04 |
| MT-ND4 | ENSG00000198886 | 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 |
| PRMT6 | ENSG00000198890 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.34 | 0.01 | 0.13 | 0.03 | 0.12 | 0.01 | 0.11 | 0.03 | 0.11 | 0.03 | 0.06 | 0.00 | 0.06 | 0.01 | 0.07 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.25 | 0.00 | 0.00 | 0.05 | 0.11 | 0.13 | 0.15 | 0.03 | 0.07 | 0.03 | 0.02 | 0.01 | 0.06 | 0.04 | 0.10 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.05 | 0.10 |
| MT-ATP6 | ENSG00000198899 | 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 |
| L1CAM | ENSG00000198910 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.12 | 0.04 | 0.06 | 0.00 | 0.06 | 0.01 | 0.23 | 0.01 | 0.19 | 0.02 | 0.14 | 0.01 | 0.27 | 0.01 | 0.17 | 0.02 | 0.05 | 0.01 | 0.10 | 0.01 | 0.06 | 0.00 | 0.14 | 0.03 | 0.10 | 0.01 | 0.15 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.12 | 0.03 | 0.46 | 0.09 | 0.22 | 0.02 | 0.12 | 0.03 | 0.09 | 0.07 | 0.25 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.15 | 0.07 | 0.02 | 0.03 | 0.03 | 0.01 | 0.05 | 0.00 | 0.06 | 0.01 |
| APRT | ENSG00000198931 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.01 | 0.25 | 0.08 | 0.05 | 0.00 | 0.00 | 0.00 | 0.19 | 0.02 | 0.12 | 0.03 | 0.06 | 0.04 | 0.04 | 0.09 | 0.05 | 0.05 | 0.05 | 0.02 | 0.03 | 0.02 | 0.03 | 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 | 0.09 | 0.05 | 0.34 | 0.05 | 0.08 | 0.02 | 0.08 | 0.03 | 0.29 | 0.06 | 0.10 | 0.00 | 0.12 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.02 | 0.02 | 0.10 |
| DMD | ENSG00000198947 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.09 | 0.04 | 0.04 | 0.09 | 0.11 | 0.03 | 0.06 | 0.12 | 0.55 | 0.04 | 0.24 | 0.00 | 0.02 | 0.03 | 0.02 | 0.00 | 0.06 | 0.01 | 0.02 | 0.00 | 0.01 | 0.05 | 0.02 | 0.01 | 0.08 | 0.00 | 0.00 | 0.03 | 0.04 | 0.10 | 0.35 | 0.03 | 0.06 | 0.04 | 0.17 | 0.10 | 0.52 | 0.25 | 0.16 | 0.05 | 0.08 | 0.00 | 0.01 | 0.06 | 0.12 | 0.01 | 0.03 | 0.05 | 0.04 | 0.00 | 0.00 | 0.04 | 0.07 |
| NAGA | ENSG00000198951 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.08 | 0.00 | 0.03 | 0.00 | 0.04 | 0.04 | 0.03 | 0.06 | 0.02 | 0.02 | 0.01 | 0.04 | 0.00 | 0.02 | 0.02 | 0.00 | 0.03 | 0.01 | 0.05 | 0.03 | 0.04 | 0.03 | 0.02 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.03 | 0.04 | 0.01 | 0.32 | 0.03 | 0.05 | 0.02 | 0.07 | 0.10 | 0.23 | 0.06 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.09 | 0.00 | 0.03 | 0.00 | 0.07 | 0.00 | 0.00 | 0.27 | 0.01 |
| TGM2 | ENSG00000198959 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.03 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.03 | 0.10 | 0.02 | 0.03 | 0.01 | 0.07 | 0.01 | 0.08 | 0.00 | 0.07 | 0.00 | 0.17 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.10 | 0.06 | 0.05 | 0.02 | 0.04 | 0.01 | 0.08 | 0.03 | 0.12 | 0.05 | 0.01 | 0.01 | 0.00 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 |
| OR10R2 | ENSG00000198965 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.41 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.28 | 0.00 | 0.25 | 0.00 | 0.06 | 0.01 | 0.25 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.29 | 0.00 | 0.41 | 0.01 | 0.18 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.38 | 0.02 | 0.15 | 0.00 | 0.14 | 0.00 | 0.29 | 0.00 | 0.36 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.16 | 0.02 |
| OR10Z1 | ENSG00000198967 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.41 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.28 | 0.00 | 0.25 | 0.00 | 0.06 | 0.00 | 0.24 | 0.00 | 0.13 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.29 | 0.00 | 0.35 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.23 | 0.01 | 0.38 | 0.02 | 0.15 | 0.00 | 0.13 | 0.00 | 0.28 | 0.00 | 0.39 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 |
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