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 |
| OR2AP1 | ENSG00000179615 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.08 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.06 | 0.03 | 0.10 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.01 | 0.17 | 0.01 | 0.18 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.18 | 0.05 | 0.03 | 0.00 | 0.07 | 0.01 | 0.12 | 0.09 | 0.30 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.04 | 0.05 | 0.00 | 0.00 | 0.05 | 0.03 |
| OR6C4 | ENSG00000179626 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.08 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.07 | 0.03 | 0.10 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.18 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.16 | 0.05 | 0.03 | 0.00 | 0.07 | 0.01 | 0.12 | 0.09 | 0.27 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.04 | 0.05 | 0.00 | 0.00 | 0.04 | 0.03 |
| OR6C2 | ENSG00000179695 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.07 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.06 | 0.03 | 0.09 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.18 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.15 | 0.05 | 0.03 | 0.00 | 0.06 | 0.01 | 0.12 | 0.09 | 0.36 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.04 | 0.05 | 0.00 | 0.00 | 0.05 | 0.03 |
| SYCN | ENSG00000179751 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.28 | 0.02 | 0.00 | 0.00 | 0.08 | 0.01 | 0.17 | 0.03 | 0.54 | 0.03 | 0.09 | 0.01 | 0.09 | 0.03 | 0.13 | 0.02 | 0.07 | 0.01 | 0.01 | 0.01 | 0.27 | 0.00 | 0.04 | 0.02 | 0.12 | 0.01 | 0.06 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.14 | 0.03 | 0.77 | 0.13 | 0.26 | 0.03 | 0.19 | 0.03 | 1.17 | 0.09 | 0.25 | 0.09 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.04 | 0.05 | 0.05 | 0.04 | 0.00 | 0.00 | 0.04 | 0.01 |
| MRGPRX4 | ENSG00000179817 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.01 | 0.01 | 0.01 | 0.07 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.04 | 0.06 | 0.07 | 0.01 | 0.05 | 0.04 | 0.03 | 0.02 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.02 | 0.03 | 0.01 | 0.00 | 0.02 | 0.06 | 0.04 | 0.00 | 0.00 | 0.06 | 0.05 | 0.05 | 0.24 | 0.01 | 0.04 | 0.03 | 0.04 | 0.01 | 0.04 | 0.09 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 |
| PDXDC1 | ENSG00000179889 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.11 | 0.06 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.03 | 0.02 | 0.04 | 0.03 | 0.05 | 0.02 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 | 0.19 | 0.07 | 0.09 | 0.00 | 0.05 | 0.01 | 0.16 | 0.00 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.04 | 0.01 |
| OR10A7 | ENSG00000179919 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.06 | 0.03 | 0.08 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.14 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.14 | 0.04 | 0.06 | 0.00 | 0.05 | 0.01 | 0.12 | 0.09 | 0.29 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.06 | 0.05 | 0.08 | 0.00 | 0.06 | 0.03 |
| GPBAR1 | ENSG00000179921 | 0.02 | 0.07 | 0.04 | 0.04 | 0.00 | 0.03 | 0.02 | 0.01 | 0.01 | 0.26 | 0.00 | 0.00 | 0.00 | 0.12 | 0.03 | 0.03 | 0.05 | 0.19 | 0.01 | 0.18 | 0.03 | 0.13 | 0.07 | 0.03 | 0.02 | 0.01 | 0.02 | 0.02 | 0.05 | 0.03 | 0.03 | 0.05 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.19 | 0.16 | 0.03 | 0.34 | 0.07 | 0.05 | 0.12 | 0.05 | 0.08 | 0.21 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.02 | 0.02 | 0.03 |
| CCR8 | ENSG00000179934 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.10 | 0.05 | 0.00 | 0.02 | 0.02 | 0.30 | 0.01 | 0.04 | 0.02 | 0.05 | 0.00 | 0.04 | 0.03 | 0.04 | 0.05 | 0.07 | 0.00 | 0.02 | 0.04 | 0.02 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.20 | 0.01 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.10 | 0.11 | 0.16 | 0.02 | 0.03 | 0.04 | 0.04 | 0.10 | 0.13 | 0.08 | 0.07 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| SSC5D | ENSG00000179954 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.21 | 0.03 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.06 | 0.12 | 0.08 | 0.06 | 0.02 | 0.12 | 0.03 | 0.13 | 0.02 | 0.03 | 0.03 | 0.01 | 0.04 | 0.05 | 0.04 | 0.06 | 0.02 | 0.02 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.18 | 0.03 | 0.16 | 0.28 | 0.14 | 0.05 | 0.06 | 0.05 | 0.42 | 0.10 | 0.05 | 0.19 | 0.00 | 0.06 | 0.01 | 0.00 | 0.26 | 0.03 | 0.01 | 0.19 | 0.03 | 0.12 | 0.00 | 0.00 | 0.03 | 0.05 |
| ZADH2 | ENSG00000180011 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.12 | 0.02 | 0.12 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.10 | 0.03 | 0.11 | 0.04 | 0.17 | 0.06 | 0.19 | 0.04 | 0.15 | 0.01 | 0.11 | 0.01 | 0.09 | 0.00 | 0.06 | 0.04 | 0.06 | 0.00 | 0.18 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.08 | 0.09 | 0.44 | 0.02 | 0.06 | 0.02 | 0.08 | 0.01 | 0.10 | 0.17 | 0.09 | 0.00 | 0.10 | 0.00 | 0.01 | 0.08 | 0.05 | 0.01 | 0.03 | 0.01 | 0.06 | 0.00 | 0.04 | 0.02 | 0.04 |
| OR1E1 | ENSG00000180016 | 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 | 0.06 | 0.02 | 0.02 | 0.01 | 0.03 | 0.04 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.12 | 0.00 | 0.08 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.13 | 0.10 | 0.01 | 0.03 | 0.03 | 0.04 | 0.06 | 0.13 | 0.15 | 0.23 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 |
| OR3A4P | ENSG00000180068 | 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 | 0.04 | 0.04 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.12 | 0.00 | 0.08 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.13 | 0.10 | 0.01 | 0.03 | 0.03 | 0.04 | 0.06 | 0.13 | 0.16 | 0.23 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 |
| WFDC11 | ENSG00000180083 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.07 | 0.01 | 0.01 | 0.01 | 0.06 | 0.00 | 0.17 | 0.01 | 0.18 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.02 | 0.20 | 0.04 | 0.02 | 0.04 | 0.09 | 0.01 | 0.29 | 0.00 | 0.12 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.01 |
| OR3A1 | ENSG00000180090 | 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 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.12 | 0.00 | 0.08 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.05 | 0.14 | 0.10 | 0.01 | 0.03 | 0.03 | 0.04 | 0.06 | 0.13 | 0.16 | 0.23 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.03 |
| TDRD6 | ENSG00000180113 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.04 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.01 | 0.16 | 0.04 | 0.06 | 0.02 | 0.27 | 0.03 | 0.17 | 0.01 | 0.05 | 0.00 | 0.11 | 0.01 | 0.01 | 0.00 | 0.08 | 0.00 | 0.05 | 0.08 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.22 | 0.07 | 0.07 | 0.03 | 0.05 | 0.01 | 0.03 | 0.03 | 0.09 | 0.03 | 0.02 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.06 | 0.01 |
| CSNK1A1L | ENSG00000180138 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.26 | 0.07 | 0.16 | 0.00 | 0.02 | 0.00 | 0.18 | 0.03 | 0.08 | 0.02 | 0.10 | 0.02 | 0.16 | 0.07 | 0.07 | 0.14 | 0.03 | 0.13 | 0.02 | 0.18 | 0.02 | 0.01 | 0.01 | 0.00 | 0.19 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.11 | 0.06 | 0.19 | 0.01 | 0.21 | 0.02 | 0.05 | 0.07 | 0.23 | 0.09 | 0.24 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.06 | 0.00 | 0.09 | 0.00 | 0.00 | 0.04 | 0.03 |
| TH | ENSG00000180176 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.01 | 0.11 | 0.00 | 0.00 | 0.02 | 0.05 | 0.03 | 0.07 | 0.01 | 0.16 | 0.02 | 0.07 | 0.02 | 0.15 | 0.06 | 0.06 | 0.20 | 0.01 | 0.23 | 0.03 | 0.01 | 0.06 | 0.04 | 0.03 | 0.03 | 0.01 | 0.08 | 0.05 | 0.04 | 0.06 | 0.00 | 0.00 | 0.03 | 0.12 | 0.05 | 0.47 | 0.01 | 0.07 | 0.04 | 0.08 | 0.23 | 0.09 | 0.04 | 0.16 | 0.02 | 0.04 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.10 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.04 |
| RRH | ENSG00000180245 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.03 | 0.03 | 0.05 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.09 | 0.00 | 0.11 | 0.12 | 0.02 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.05 | 0.04 | 0.26 | 0.01 | 0.01 | 0.02 | 0.04 | 0.00 | 0.11 | 0.08 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 |
| SLC9A4 | ENSG00000180251 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.10 | 0.01 | 0.07 | 0.01 | 0.19 | 0.02 | 0.08 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.16 | 0.07 | 0.03 | 0.01 | 0.04 | 0.01 | 0.09 | 0.00 | 0.14 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
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