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 |
| OR52A5 | ENSG00000171944 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.09 | 0.00 | 0.00 | 0.05 | 0.05 | 0.01 | 0.06 | 0.02 | 0.14 | 0.01 | 0.06 | 0.04 | 0.10 | 0.02 | 0.05 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.03 | 0.03 | 0.03 | 0.01 | 0.01 | 0.07 | 0.03 | 0.07 | 0.00 | 0.00 | 0.02 | 0.10 | 0.01 | 0.43 | 0.01 | 0.05 | 0.02 | 0.07 | 0.03 | 0.09 | 0.04 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.10 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.03 |
| CYP4F22 | ENSG00000171954 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.02 | 0.11 | 0.02 | 0.07 | 0.01 | 0.25 | 0.01 | 0.07 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.13 | 0.03 | 0.00 | 0.03 | 0.35 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.80 | 0.04 | 0.01 | 0.01 | 0.25 | 0.01 | 0.36 | 0.05 | 0.17 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 |
| PPIH | ENSG00000171960 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.19 | 0.03 | 0.00 | 0.00 | 0.08 | 0.03 | 0.12 | 0.02 | 0.10 | 0.02 | 0.08 | 0.01 | 0.14 | 0.01 | 0.05 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.06 | 0.00 | 0.02 | 0.09 | 0.00 | 0.22 | 0.00 | 0.03 | 0.02 | 0.08 | 0.00 | 0.00 | 0.11 | 0.04 | 0.62 | 0.06 | 0.10 | 0.00 | 0.12 | 0.01 | 0.13 | 0.05 | 0.12 | 0.04 | 0.05 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.07 | 0.05 | 0.03 |
| REG1B | ENSG00000172023 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.10 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.13 | 0.02 | 0.05 | 0.02 | 0.08 | 0.04 | 0.03 | 0.03 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.12 | 0.05 | 0.03 | 0.01 | 0.05 | 0.01 | 0.16 | 0.06 | 0.11 | 0.04 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 |
| LAMB2 | ENSG00000172037 | 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 | 0.09 | 0.00 | 0.06 | 0.00 | 0.12 | 0.01 | 0.11 | 0.00 | 0.05 | 0.02 | 0.09 | 0.00 | 0.04 | 0.04 | 0.05 | 0.00 | 0.24 | 0.04 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.17 | 0.07 | 0.20 | 0.00 | 0.06 | 0.04 | 0.05 | 0.06 | 0.31 | 0.02 | 0.16 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.11 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.03 | 0.01 | 0.04 |
| SMN1 | ENSG00000172062 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.23 | 0.00 | 0.16 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.08 | 0.02 | 0.10 | 0.01 | 0.08 | 0.02 | 0.16 | 0.02 | 0.14 | 0.00 | 0.07 | 0.00 | 0.06 | 0.00 | 0.07 | 0.01 | 0.04 | 0.00 | 0.13 | 0.06 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.10 | 0.03 | 0.74 | 0.00 | 0.06 | 0.02 | 0.11 | 0.00 | 0.35 | 0.02 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| SLC9C1 | ENSG00000172139 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.14 | 0.03 | 0.05 | 0.01 | 0.08 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.10 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.06 | 0.02 | 0.39 | 0.04 | 0.05 | 0.01 | 0.04 | 0.01 | 0.03 | 0.08 | 0.10 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
| OR1A1 | ENSG00000172146 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.07 | 0.02 | 0.02 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.13 | 0.00 | 0.03 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.14 | 0.09 | 0.01 | 0.03 | 0.03 | 0.04 | 0.06 | 0.13 | 0.16 | 0.22 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 |
| AC005255.6 | ENSG00000172148 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.03 | 0.13 | 0.03 | 0.06 | 0.01 | 0.15 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.07 | 0.04 | 0.00 | 0.03 | 0.34 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.11 | 0.03 | 0.84 | 0.05 | 0.05 | 0.02 | 0.22 | 0.01 | 0.26 | 0.09 | 0.16 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.04 | 0.01 |
| OR1A2 | ENSG00000172150 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.07 | 0.02 | 0.02 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.13 | 0.00 | 0.03 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.14 | 0.09 | 0.01 | 0.03 | 0.03 | 0.04 | 0.06 | 0.13 | 0.16 | 0.22 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 |
| OR8I2 | ENSG00000172154 | 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 |
| CCL11 | ENSG00000172156 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.15 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.06 | 0.01 | 0.04 | 0.06 | 0.05 | 0.03 | 0.14 | 0.06 | 0.15 | 0.01 | 0.07 | 0.02 | 0.06 | 0.01 | 0.05 | 0.02 | 0.04 | 0.04 | 0.05 | 0.01 | 0.01 | 0.10 | 0.00 | 0.14 | 0.00 | 0.00 | 0.11 | 0.11 | 0.09 | 0.21 | 0.00 | 0.03 | 0.04 | 0.07 | 0.11 | 0.13 | 0.05 | 0.17 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.05 | 0.04 | 0.03 |
| OR4C11 | ENSG00000172188 | 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 |
| OR8U1 | ENSG00000172199 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.14 | 0.03 | 0.00 | 0.00 | 0.06 | 0.03 | 0.03 | 0.03 | 0.09 | 0.03 | 0.12 | 0.01 | 0.16 | 0.03 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.02 | 0.05 | 0.07 | 0.05 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.07 | 0.11 | 0.04 | 0.05 | 0.01 | 0.04 | 0.02 | 0.28 | 0.02 | 0.07 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 |
| OR4X2 | ENSG00000172208 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.06 | 0.04 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.07 | 0.03 | 0.05 | 0.01 | 0.08 | 0.04 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.07 | 0.07 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.03 | 0.10 | 0.06 | 0.05 | 0.03 | 0.03 | 0.02 | 0.05 | 0.07 | 0.09 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.00 | 0.02 | 0.01 | 0.04 |
| GPR22 | ENSG00000172209 | 0.02 | 0.00 | 0.04 | 0.01 | 0.01 | 0.00 | 0.03 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.10 | 0.03 | 0.14 | 0.03 | 0.15 | 0.03 | 0.35 | 0.08 | 0.12 | 0.04 | 0.01 | 0.00 | 0.01 | 0.02 | 0.03 | 0.03 | 0.07 | 0.02 | 0.00 | 0.02 | 0.02 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.25 | 0.06 | 0.04 | 0.02 | 0.02 | 0.03 | 0.12 | 0.05 | 0.16 | 0.02 | 0.08 | 0.02 | 0.00 | 0.02 | 0.13 | 0.00 | 0.09 | 0.00 | 0.02 | 0.01 | 0.00 | 0.03 | 0.08 | 0.03 |
| CXCR6 | ENSG00000172215 | 0.00 | 0.18 | 0.00 | 0.02 | 0.08 | 0.00 | 0.00 | 0.02 | 0.08 | 0.10 | 0.00 | 0.03 | 0.00 | 0.51 | 0.01 | 0.06 | 0.01 | 0.08 | 0.00 | 0.05 | 0.02 | 0.08 | 0.01 | 0.09 | 0.00 | 0.04 | 0.03 | 0.06 | 0.00 | 0.04 | 0.04 | 0.03 | 0.00 | 0.24 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.07 | 0.18 | 0.01 | 0.05 | 0.01 | 0.05 | 0.02 | 0.20 | 0.04 | 0.13 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.02 | 0.05 |
| TPSAB1 | ENSG00000172236 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.05 | 0.04 | 0.09 | 0.03 | 0.03 | 0.03 | 0.12 | 0.04 | 0.08 | 0.03 | 0.04 | 0.03 | 0.03 | 0.01 | 0.02 | 0.04 | 0.06 | 0.00 | 0.05 | 0.18 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.11 | 0.19 | 0.10 | 0.05 | 0.04 | 0.04 | 0.17 | 0.21 | 0.08 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 |
| CDY1 | ENSG00000172288 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| OR10V1 | ENSG00000172289 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.02 | 0.01 | 0.12 | 0.02 | 0.00 | 0.00 | 0.07 | 0.04 | 0.04 | 0.02 | 0.08 | 0.02 | 0.10 | 0.03 | 0.09 | 0.04 | 0.02 | 0.04 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.02 | 0.04 | 0.07 | 0.06 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.07 | 0.12 | 0.05 | 0.05 | 0.02 | 0.06 | 0.01 | 0.15 | 0.13 | 0.04 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.04 |
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