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 |
| ADGRD2 | ENSG00000180264 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.05 | 0.03 | 0.06 | 0.01 | 0.10 | 0.02 | 0.08 | 0.01 | 0.01 | 0.01 | 0.05 | 0.02 | 0.00 | 0.01 | 0.03 | 0.03 | 0.06 | 0.04 | 0.15 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.03 | 0.11 | 0.14 | 0.02 | 0.01 | 0.01 | 0.04 | 0.02 | 0.16 | 0.11 | 0.04 | 0.01 | 0.02 | 0.01 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 |
| GPR139 | ENSG00000180269 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.01 | 0.05 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.16 | 0.03 | 0.05 | 0.00 | 0.07 | 0.01 | 0.09 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| FZD2 | ENSG00000180340 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.04 | 0.03 | 0.01 | 0.00 | 0.03 | 0.00 | 0.06 | 0.01 | 0.05 | 0.05 | 0.01 | 0.01 | 0.12 | 0.03 | 0.06 | 0.03 | 0.03 | 0.00 | 0.03 | 0.03 | 0.05 | 0.01 | 0.03 | 0.03 | 0.02 | 0.01 | 0.01 | 0.11 | 0.00 | 0.08 | 0.00 | 0.00 | 0.03 | 0.10 | 0.02 | 0.12 | 0.02 | 0.02 | 0.03 | 0.07 | 0.10 | 0.18 | 0.06 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.05 |
| CYP8B1 | ENSG00000180432 | 0.00 | 0.18 | 0.00 | 0.02 | 0.08 | 0.00 | 0.01 | 0.01 | 0.06 | 0.08 | 0.00 | 0.03 | 0.01 | 0.41 | 0.01 | 0.04 | 0.00 | 0.07 | 0.00 | 0.05 | 0.01 | 0.04 | 0.03 | 0.08 | 0.00 | 0.03 | 0.04 | 0.05 | 0.00 | 0.03 | 0.07 | 0.02 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.13 | 0.08 | 0.17 | 0.02 | 0.04 | 0.02 | 0.04 | 0.02 | 0.19 | 0.06 | 0.10 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.10 | 0.01 | 0.04 | 0.02 | 0.04 | 0.00 | 0.03 | 0.02 | 0.04 |
| OR6K6 | ENSG00000180433 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.06 | 0.41 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.27 | 0.00 | 0.25 | 0.00 | 0.06 | 0.00 | 0.24 | 0.00 | 0.11 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.28 | 0.00 | 0.35 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.23 | 0.01 | 0.37 | 0.02 | 0.15 | 0.00 | 0.13 | 0.00 | 0.28 | 0.00 | 0.37 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.15 | 0.02 |
| OR6K4P | ENSG00000180437 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.06 | 0.41 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.27 | 0.00 | 0.25 | 0.00 | 0.06 | 0.00 | 0.24 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.28 | 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 | 0.38 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.16 | 0.02 |
| OR10Q1 | ENSG00000180475 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.00 | 0.00 | 0.02 | 0.14 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.04 | 0.04 | 0.07 | 0.02 | 0.11 | 0.02 | 0.12 | 0.05 | 0.01 | 0.04 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.12 | 0.04 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.10 | 0.07 | 0.12 | 0.05 | 0.05 | 0.02 | 0.06 | 0.02 | 0.24 | 0.13 | 0.06 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.09 | 0.03 |
| KCNE1 | ENSG00000180509 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.07 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.03 | 0.02 | 0.04 | 0.04 | 0.03 | 0.01 | 0.01 | 0.04 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.02 | 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 | 0.05 | 0.03 | 0.02 | 0.01 | 0.03 | 0.03 | 0.04 | 0.07 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 |
| SSTR2 | ENSG00000180616 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.21 | 0.00 | 0.02 | 0.00 | 0.09 | 0.02 | 0.16 | 0.01 | 0.23 | 0.01 | 0.08 | 0.03 | 0.19 | 0.06 | 0.14 | 0.03 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.10 | 0.23 | 0.01 | 0.08 | 0.01 | 0.07 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.39 | 0.02 | 0.28 | 0.03 | 0.15 | 0.03 | 0.10 | 0.01 | 0.32 | 0.03 | 0.22 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.00 | 0.03 | 0.02 | 0.14 | 0.01 | 0.24 | 0.01 |
| PRF1 | ENSG00000180644 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.03 | 0.03 | 0.02 | 0.05 | 0.05 | 0.10 | 0.02 | 0.02 | 0.03 | 0.04 | 0.03 | 0.01 | 0.00 | 0.02 | 0.02 | 0.25 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.03 | 0.13 | 0.11 | 0.00 | 0.01 | 0.08 | 0.03 | 0.15 | 0.03 | 0.03 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 |
| OR2A4 | ENSG00000180658 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.02 | 0.07 | 0.05 | 0.00 | 0.01 | 0.00 | 0.17 | 0.03 | 0.04 | 0.06 | 0.03 | 0.04 | 0.02 | 0.10 | 0.03 | 0.06 | 0.04 | 0.02 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.02 | 0.09 | 0.00 | 0.10 | 0.04 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.05 | 0.08 | 0.27 | 0.01 | 0.02 | 0.06 | 0.03 | 0.08 | 0.03 | 0.25 | 0.06 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.05 | 0.00 | 0.11 | 0.00 | 0.05 | 0.01 | 0.12 |
| YOD1 | ENSG00000180667 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.01 | 0.12 | 0.01 | 0.09 | 0.01 | 0.05 | 0.00 | 0.19 | 0.06 | 0.12 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.22 | 0.11 | 0.07 | 0.00 | 0.07 | 0.02 | 0.17 | 0.04 | 0.05 | 0.18 | 0.03 | 0.02 | 0.01 | 0.00 | 0.16 | 0.10 | 0.00 | 0.01 | 0.04 | 0.02 | 0.09 | 0.00 | 0.15 | 0.02 |
| OR10K2 | ENSG00000180708 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.40 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.27 | 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 | 0.38 | 0.02 | 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 | 0.01 |
| CHRM4 | ENSG00000180720 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.09 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.02 | 0.14 | 0.03 | 0.11 | 0.01 | 0.16 | 0.03 | 0.15 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.05 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.07 | 0.02 | 0.13 | 0.06 | 0.08 | 0.02 | 0.11 | 0.01 | 0.03 | 0.03 | 0.10 | 0.07 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.02 | 0.07 | 0.00 | 0.02 | 0.01 | 0.05 |
| SHISA2 | ENSG00000180730 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.11 | 0.05 | 0.00 | 0.02 | 0.00 | 0.17 | 0.01 | 0.11 | 0.02 | 0.12 | 0.03 | 0.13 | 0.08 | 0.09 | 0.08 | 0.04 | 0.24 | 0.01 | 0.23 | 0.02 | 0.00 | 0.00 | 0.03 | 0.11 | 0.00 | 0.15 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.09 | 0.06 | 0.07 | 0.18 | 0.02 | 0.13 | 0.01 | 0.05 | 0.01 | 0.16 | 0.12 | 0.19 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.06 | 0.01 | 0.06 | 0.00 | 0.00 | 0.05 | 0.04 |
| CHST13 | ENSG00000180767 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.05 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.11 | 0.02 | 0.05 | 0.00 | 0.10 | 0.04 | 0.06 | 0.02 | 0.00 | 0.00 | 0.04 | 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 | 0.03 | 0.04 | 0.23 | 0.04 | 0.08 | 0.00 | 0.05 | 0.00 | 0.09 | 0.07 | 0.06 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 |
| AGTR2 | ENSG00000180772 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.03 | 0.03 | 0.00 | 0.00 | 0.01 | 0.06 | 0.01 | 0.10 | 0.01 | 0.05 | 0.01 | 0.14 | 0.01 | 0.06 | 0.03 | 0.03 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.07 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.10 | 0.05 | 0.07 | 0.01 | 0.02 | 0.01 | 0.01 | 0.02 | 0.09 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| SLC36A4 | ENSG00000180773 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.03 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.06 | 0.08 | 0.08 | 0.03 | 0.07 | 0.09 | 0.10 | 0.09 | 0.14 | 0.04 | 0.05 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.13 | 0.31 | 0.10 | 0.13 | 0.07 | 0.05 | 0.03 | 0.08 | 0.16 | 0.08 | 0.13 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.09 |
| OR51E1 | ENSG00000180785 | 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 | 0.04 |
| ARSJ | ENSG00000180801 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.01 | 0.04 | 0.04 | 0.02 | 0.05 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.02 | 0.02 | 0.10 | 0.00 | 0.11 | 0.11 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.06 | 0.27 | 0.01 | 0.02 | 0.02 | 0.05 | 0.00 | 0.11 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.06 |
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