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 |
| KCNS3 | ENSG00000170745 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.11 | 0.01 | 0.00 | 0.00 | 0.03 | 0.08 | 0.05 | 0.02 | 0.11 | 0.04 | 0.03 | 0.03 | 0.04 | 0.06 | 0.03 | 0.04 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.04 | 0.12 | 0.01 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.05 | 0.22 | 0.15 | 0.09 | 0.01 | 0.11 | 0.03 | 0.37 | 0.03 | 0.03 | 0.10 | 0.16 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.05 | 0.03 | 0.05 | 0.00 | 0.03 | 0.04 |
| GPR37 | ENSG00000170775 | 0.01 | 0.01 | 0.07 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.03 | 0.04 | 0.00 | 0.01 | 0.04 | 0.07 | 0.06 | 0.03 | 0.08 | 0.06 | 0.03 | 0.11 | 0.04 | 0.17 | 0.03 | 0.07 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.05 | 0.04 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.04 | 0.28 | 0.05 | 0.04 | 0.07 | 0.02 | 0.05 | 0.06 | 0.12 | 0.13 | 0.06 | 0.03 | 0.02 | 0.00 | 0.05 | 0.06 | 0.07 | 0.10 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 |
| OR10A4 | ENSG00000170782 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.00 | 0.02 | 0.07 | 0.02 | 0.06 | 0.02 | 0.13 | 0.01 | 0.06 | 0.05 | 0.12 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.03 | 0.02 | 0.03 | 0.01 | 0.01 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.03 | 0.10 | 0.01 | 0.41 | 0.01 | 0.05 | 0.02 | 0.07 | 0.03 | 0.18 | 0.03 | 0.13 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.09 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.03 |
| SDR16C5 | ENSG00000170786 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.05 | 0.01 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.12 | 0.02 | 0.12 | 0.03 | 0.04 | 0.01 | 0.08 | 0.03 | 0.07 | 0.02 | 0.07 | 0.01 | 0.10 | 0.01 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.16 | 0.02 | 0.42 | 0.03 | 0.03 | 0.01 | 0.11 | 0.00 | 0.73 | 0.09 | 0.15 | 0.04 | 0.21 | 0.00 | 0.01 | 0.00 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.20 | 0.00 | 0.06 | 0.01 |
| OR10A2 | ENSG00000170790 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.03 | 0.02 | 0.07 | 0.02 | 0.06 | 0.02 | 0.14 | 0.01 | 0.06 | 0.05 | 0.12 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.03 | 0.02 | 0.03 | 0.01 | 0.01 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.04 | 0.10 | 0.01 | 0.41 | 0.01 | 0.05 | 0.02 | 0.06 | 0.03 | 0.18 | 0.03 | 0.13 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.01 | 0.09 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.02 |
| FSHR | ENSG00000170820 | 0.00 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.01 | 0.25 | 0.01 | 0.04 | 0.01 | 0.06 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.08 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.01 | 0.25 | 0.03 | 0.03 | 0.01 | 0.04 | 0.02 | 0.04 | 0.02 | 0.08 | 0.06 | 0.11 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.01 |
| GPR27 | ENSG00000170837 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.16 | 0.04 | 0.17 | 0.00 | 0.04 | 0.01 | 0.11 | 0.04 | 0.05 | 0.00 | 0.18 | 0.02 | 0.08 | 0.04 | 0.16 | 0.10 | 0.05 | 0.01 | 0.01 | 0.03 | 0.03 | 0.06 | 0.02 | 0.02 | 0.08 | 0.00 | 0.21 | 0.08 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.11 | 0.12 | 0.02 | 0.13 | 0.03 | 0.07 | 0.25 | 0.24 | 0.03 | 0.09 | 0.10 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.03 | 0.18 | 0.01 |
| MINA | ENSG00000170854 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.05 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.02 | 0.19 | 0.03 | 0.07 | 0.01 | 0.10 | 0.04 | 0.05 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.12 | 0.10 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.22 | 0.05 | 0.07 | 0.01 | 0.04 | 0.00 | 0.18 | 0.08 | 0.08 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 |
| TRIAP1 | ENSG00000170855 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.04 | 0.10 | 0.04 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.03 | 0.05 | 0.03 | 0.02 | 0.09 | 0.05 | 0.07 | 0.02 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.06 | 0.02 | 0.07 | 0.00 | 0.17 | 0.16 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.08 | 0.14 | 0.20 | 0.02 | 0.02 | 0.05 | 0.04 | 0.09 | 0.12 | 0.13 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.07 | 0.00 | 0.02 | 0.06 |
| PLA2G1B | ENSG00000170890 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.04 | 0.09 | 0.04 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.03 | 0.05 | 0.03 | 0.02 | 0.10 | 0.05 | 0.07 | 0.02 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.06 | 0.03 | 0.07 | 0.00 | 0.17 | 0.13 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.08 | 0.14 | 0.20 | 0.01 | 0.02 | 0.05 | 0.04 | 0.09 | 0.08 | 0.13 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.07 | 0.00 | 0.02 | 0.06 |
| CYTL1 | ENSG00000170891 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.02 | 0.06 | 0.04 | 0.07 | 0.04 | 0.05 | 0.02 | 0.03 | 0.03 | 0.03 | 0.03 | 0.01 | 0.04 | 0.05 | 0.00 | 0.01 | 0.08 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.05 | 0.24 | 0.07 | 0.02 | 0.05 | 0.06 | 0.04 | 0.12 | 0.00 | 0.12 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.05 |
| TRH | ENSG00000170893 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.14 | 0.01 | 0.07 | 0.00 | 0.17 | 0.03 | 0.06 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.03 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.06 | 0.03 | 0.28 | 0.04 | 0.09 | 0.01 | 0.09 | 0.00 | 0.15 | 0.03 | 0.05 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.05 |
| GSTA4 | ENSG00000170899 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.04 | 0.00 | 0.00 | 0.00 | 0.03 | 0.06 | 0.01 | 0.21 | 0.04 | 0.11 | 0.02 | 0.25 | 0.04 | 0.18 | 0.01 | 0.02 | 0.01 | 0.09 | 0.02 | 0.01 | 0.00 | 0.09 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.18 | 0.06 | 0.09 | 0.04 | 0.05 | 0.01 | 0.17 | 0.03 | 0.09 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.02 |
| OR7G3 | ENSG00000170920 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.00 | 0.01 | 0.05 | 0.02 | 0.01 | 0.06 | 0.07 | 0.07 | 0.06 | 0.05 | 0.03 | 0.09 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.03 | 0.01 | 0.12 | 0.00 | 0.01 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.05 | 0.44 | 0.27 | 0.10 | 0.09 | 0.14 | 0.13 | 0.31 | 0.32 | 0.20 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.02 | 0.04 | 0.01 |
| OR7G2 | ENSG00000170923 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.00 | 0.01 | 0.05 | 0.02 | 0.01 | 0.06 | 0.07 | 0.07 | 0.06 | 0.05 | 0.02 | 0.09 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.03 | 0.01 | 0.12 | 0.00 | 0.01 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.05 | 0.44 | 0.27 | 0.10 | 0.09 | 0.14 | 0.13 | 0.34 | 0.32 | 0.20 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 |
| OR1M1 | ENSG00000170929 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.05 | 0.00 | 0.01 | 0.05 | 0.02 | 0.01 | 0.06 | 0.07 | 0.07 | 0.06 | 0.05 | 0.02 | 0.09 | 0.04 | 0.07 | 0.01 | 0.01 | 0.00 | 0.04 | 0.02 | 0.03 | 0.01 | 0.12 | 0.00 | 0.01 | 0.06 | 0.03 | 0.01 | 0.00 | 0.00 | 0.01 | 0.08 | 0.05 | 0.44 | 0.27 | 0.08 | 0.09 | 0.14 | 0.13 | 0.34 | 0.32 | 0.20 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 |
| OR8B12 | ENSG00000170953 | 0.00 | 0.01 | 0.00 | 0.06 | 0.00 | 0.02 | 0.02 | 0.06 | 0.03 | 0.10 | 0.00 | 0.00 | 0.11 | 0.06 | 0.05 | 0.09 | 0.04 | 0.10 | 0.04 | 0.14 | 0.05 | 0.15 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.19 | 0.00 | 0.06 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.22 | 0.19 | 0.17 | 0.04 | 0.31 | 0.04 | 0.08 | 0.05 | 0.17 | 0.03 | 0.24 | 0.00 | 0.24 | 0.03 | 0.00 | 0.13 | 0.02 | 0.07 | 0.01 | 0.01 | 0.02 | 0.00 | 0.07 | 0.00 | 0.26 |
| PLAC1 | ENSG00000170965 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.07 | 0.03 | 0.05 | 0.00 | 0.06 | 0.01 | 0.13 | 0.01 | 0.09 | 0.03 | 0.06 | 0.01 | 0.12 | 0.01 | 0.15 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.04 | 0.00 | 0.08 | 0.03 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.28 | 0.05 | 0.12 | 0.00 | 0.03 | 0.01 | 0.04 | 0.10 | 0.04 | 0.15 | 0.00 | 0.02 | 0.00 | 0.01 | 0.06 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| S1PR1 | ENSG00000170989 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.38 | 0.02 | 0.12 | 0.02 | 0.10 | 0.01 | 0.08 | 0.02 | 0.10 | 0.02 | 0.06 | 0.01 | 0.07 | 0.01 | 0.06 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.11 | 0.04 | 0.04 | 0.00 | 0.25 | 0.00 | 0.00 | 0.01 | 0.11 | 0.14 | 0.18 | 0.00 | 0.07 | 0.02 | 0.02 | 0.06 | 0.06 | 0.05 | 0.09 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.03 | 0.04 | 0.11 |
| OR4D5 | ENSG00000171014 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.02 | 0.02 | 0.07 | 0.03 | 0.09 | 0.00 | 0.00 | 0.13 | 0.06 | 0.05 | 0.09 | 0.05 | 0.10 | 0.05 | 0.14 | 0.05 | 0.15 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.19 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.22 | 0.19 | 0.17 | 0.04 | 0.31 | 0.04 | 0.07 | 0.05 | 0.17 | 0.03 | 0.23 | 0.00 | 0.24 | 0.03 | 0.00 | 0.13 | 0.02 | 0.06 | 0.01 | 0.01 | 0.01 | 0.00 | 0.07 | 0.01 | 0.26 |
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