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 |
| DRD5 | ENSG00000169676 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.08 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.04 | 0.04 | 0.03 | 0.05 | 0.09 | 0.05 | 0.06 | 0.04 | 0.01 | 0.02 | 0.04 | 0.03 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.21 | 0.05 | 0.01 | 0.03 | 0.05 | 0.02 | 0.13 | 0.00 | 0.06 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.05 | 0.02 |
| BUB1 | ENSG00000169679 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.05 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.09 | 0.02 | 0.07 | 0.01 | 0.18 | 0.02 | 0.09 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.03 | 0.08 | 0.13 | 0.05 | 0.02 | 0.05 | 0.03 | 0.09 | 0.00 | 0.14 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| CHRNA5 | ENSG00000169684 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.03 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.01 | 0.09 | 0.01 | 0.03 | 0.02 | 0.07 | 0.03 | 0.06 | 0.03 | 0.03 | 0.01 | 0.03 | 0.00 | 0.04 | 0.01 | 0.04 | 0.03 | 0.05 | 0.01 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.18 | 0.12 | 0.12 | 0.01 | 0.03 | 0.03 | 0.13 | 0.07 | 0.06 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.14 | 0.01 |
| GP9 | ENSG00000169704 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.11 | 0.01 | 0.07 | 0.00 | 0.13 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.03 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.04 | 0.27 | 0.04 | 0.09 | 0.01 | 0.08 | 0.00 | 0.17 | 0.04 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.02 | 0.05 | 0.02 | 0.01 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
| DCXR | ENSG00000169738 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.02 | 0.21 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.16 | 0.02 | 0.19 | 0.07 | 0.06 | 0.07 | 0.12 | 0.11 | 0.11 | 0.04 | 0.06 | 0.00 | 0.04 | 0.03 | 0.02 | 0.09 | 0.33 | 0.01 | 0.15 | 0.01 | 0.29 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.34 | 0.05 | 0.42 | 0.06 | 0.09 | 0.09 | 0.19 | 0.01 | 0.74 | 0.08 | 0.19 | 0.13 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.04 | 0.02 | 0.20 | 0.00 | 0.24 | 0.03 |
| NRG4 | ENSG00000169752 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.04 | 0.03 | 0.00 | 0.00 | 0.09 | 0.00 | 0.03 | 0.02 | 0.09 | 0.01 | 0.02 | 0.03 | 0.07 | 0.03 | 0.07 | 0.04 | 0.02 | 0.02 | 0.03 | 0.03 | 0.03 | 0.01 | 0.04 | 0.03 | 0.05 | 0.01 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.03 | 0.17 | 0.15 | 0.12 | 0.01 | 0.03 | 0.05 | 0.14 | 0.05 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.16 | 0.01 |
| TAS2R1 | ENSG00000169777 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.08 | 0.02 | 0.02 | 0.21 | 0.02 | 0.00 | 0.01 | 0.04 | 0.02 | 0.30 | 0.01 | 0.30 | 0.01 | 0.09 | 0.02 | 0.22 | 0.01 | 0.09 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.08 | 0.02 | 0.00 | 0.05 | 0.26 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.33 | 0.05 | 0.13 | 0.02 | 0.10 | 0.01 | 0.08 | 0.07 | 0.30 | 0.04 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.02 | 0.00 | 0.00 | 0.15 | 0.08 |
| TACR3 | ENSG00000169836 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.02 | 0.07 | 0.02 | 0.03 | 0.01 | 0.03 | 0.01 | 0.06 | 0.00 | 0.01 | 0.01 | 0.13 | 0.00 | 0.06 | 0.04 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.05 | 0.05 | 0.02 | 0.30 | 0.01 | 0.02 | 0.01 | 0.05 | 0.04 | 0.11 | 0.03 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.06 |
| P2RY1 | ENSG00000169860 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.05 | 0.03 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.11 | 0.01 | 0.87 | 0.01 | 0.44 | 0.00 | 0.53 | 0.02 | 0.11 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.07 | 0.01 | 0.09 | 0.03 | 0.09 | 0.01 | 0.00 | 0.06 | 0.00 | 0.00 | 0.16 | 0.01 | 0.67 | 0.02 | 0.41 | 0.01 | 0.15 | 0.01 | 0.23 | 0.07 | 0.05 | 0.09 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.01 | 0.02 | 0.03 | 0.00 | 0.00 | 0.03 | 0.03 |
| MUC17 | ENSG00000169876 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.07 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.10 | 0.01 | 0.22 | 0.02 | 0.21 | 0.01 | 0.47 | 0.02 | 0.18 | 0.02 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.02 | 0.06 | 0.02 | 0.11 | 0.01 | 0.08 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.04 | 0.21 | 0.05 | 0.06 | 0.02 | 0.07 | 0.02 | 0.15 | 0.03 | 0.07 | 0.04 | 0.07 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.07 | 0.00 | 0.03 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 |
| MUC3A | ENSG00000169894 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| TM4SF1 | ENSG00000169908 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.12 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.10 | 0.01 | 0.82 | 0.01 | 0.42 | 0.00 | 0.56 | 0.01 | 0.15 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.00 | 0.11 | 0.01 | 0.03 | 0.03 | 0.09 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.15 | 0.01 | 0.68 | 0.02 | 0.41 | 0.00 | 0.16 | 0.01 | 0.24 | 0.02 | 0.08 | 0.07 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 |
| TAS1R3 | ENSG00000169962 | 0.00 | 0.05 | 0.01 | 0.10 | 0.00 | 0.00 | 0.02 | 0.03 | 0.10 | 0.08 | 0.00 | 0.02 | 0.04 | 0.27 | 0.09 | 0.06 | 0.08 | 0.11 | 0.06 | 0.09 | 0.13 | 0.08 | 0.09 | 0.09 | 0.02 | 0.11 | 0.00 | 0.17 | 0.05 | 0.05 | 0.02 | 0.31 | 0.00 | 1.01 | 0.05 | 0.17 | 0.01 | 0.12 | 0.00 | 0.00 | 0.04 | 0.19 | 0.23 | 0.38 | 0.06 | 0.11 | 0.05 | 0.12 | 0.08 | 0.27 | 0.18 | 0.28 | 0.10 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.00 | 0.03 | 0.03 | 0.15 | 0.00 | 0.14 | 0.07 | 0.13 |
| NLGN2 | ENSG00000169992 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.25 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.03 | 0.02 | 0.04 | 0.03 | 0.04 | 0.01 | 0.03 | 0.00 | 0.03 | 0.00 | 0.03 | 0.01 | 0.03 | 0.00 | 0.15 | 0.01 | 0.08 | 0.03 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.07 | 0.13 | 0.04 | 0.00 | 0.03 | 0.05 | 0.02 | 0.06 | 0.18 | 0.11 | 0.38 | 0.00 | 0.02 | 0.04 | 0.02 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.05 |
| YWHAG | ENSG00000170027 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.02 | 0.12 | 0.02 | 0.05 | 0.03 | 0.16 | 0.02 | 0.12 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.05 | 0.01 | 0.00 | 0.01 | 0.12 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.17 | 0.07 | 0.05 | 0.01 | 0.07 | 0.02 | 0.14 | 0.03 | 0.05 | 0.07 | 0.09 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
| KCNAB3 | ENSG00000170049 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.24 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.01 | 0.02 | 0.01 | 0.03 | 0.03 | 0.04 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.16 | 0.00 | 0.12 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.06 | 0.08 | 0.05 | 0.00 | 0.04 | 0.03 | 0.04 | 0.06 | 0.15 | 0.15 | 0.32 | 0.00 | 0.02 | 0.02 | 0.01 | 0.00 | 0.10 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.05 |
| SERPINA9 | ENSG00000170054 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.06 | 0.12 | 0.02 | 0.05 | 0.04 | 0.07 | 0.06 | 0.03 | 0.05 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.02 | 0.02 | 0.10 | 0.00 | 0.31 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.21 | 0.17 | 0.07 | 0.09 | 0.04 | 0.03 | 0.06 | 0.02 | 0.06 | 0.09 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.02 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| SERPINA6 | ENSG00000170099 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.06 | 0.12 | 0.02 | 0.05 | 0.04 | 0.07 | 0.06 | 0.03 | 0.05 | 0.00 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.10 | 0.00 | 0.31 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.09 | 0.20 | 0.17 | 0.07 | 0.09 | 0.05 | 0.03 | 0.06 | 0.02 | 0.06 | 0.08 | 0.03 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.01 | 0.06 | 0.03 | 0.01 | 0.01 | 0.06 |
| GPR25 | ENSG00000170128 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.12 | 0.04 | 0.02 | 0.00 | 0.10 | 0.00 | 0.12 | 0.00 | 0.08 | 0.01 | 0.06 | 0.01 | 0.13 | 0.06 | 0.04 | 0.01 | 0.04 | 0.00 | 0.06 | 0.05 | 0.01 | 0.00 | 0.18 | 0.01 | 0.18 | 0.02 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.22 | 0.00 | 0.28 | 0.06 | 0.07 | 0.00 | 0.07 | 0.02 | 0.12 | 0.03 | 0.10 | 0.12 | 0.07 | 0.02 | 0.01 | 0.00 | 0.26 | 0.02 | 0.00 | 0.01 | 0.02 | 0.01 | 0.09 | 0.00 | 0.20 | 0.01 |
| GYPA | ENSG00000170180 | 0.03 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.02 | 0.01 | 0.11 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.03 | 0.11 | 0.03 | 0.04 | 0.14 | 0.04 | 0.09 | 0.04 | 0.01 | 0.02 | 0.02 | 0.02 | 0.00 | 0.02 | 0.06 | 0.05 | 0.00 | 0.03 | 0.10 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.03 | 0.11 | 0.15 | 0.03 | 0.05 | 0.03 | 0.02 | 0.04 | 0.04 | 0.11 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.03 | 0.01 | 0.07 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.03 |
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