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 |
| OR5I1 | ENSG00000167825 | 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 |
| CD300C | ENSG00000167850 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.21 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.16 | 0.02 | 0.22 | 0.01 | 0.07 | 0.03 | 0.20 | 0.06 | 0.12 | 0.03 | 0.03 | 0.01 | 0.05 | 0.04 | 0.05 | 0.10 | 0.25 | 0.00 | 0.08 | 0.01 | 0.08 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.36 | 0.04 | 0.31 | 0.03 | 0.20 | 0.03 | 0.14 | 0.01 | 0.39 | 0.03 | 0.24 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.05 | 0.01 | 0.14 | 0.01 | 0.24 | 0.02 |
| CD300A | ENSG00000167851 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.21 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.16 | 0.02 | 0.22 | 0.01 | 0.07 | 0.03 | 0.20 | 0.06 | 0.12 | 0.03 | 0.03 | 0.01 | 0.05 | 0.04 | 0.05 | 0.10 | 0.25 | 0.00 | 0.08 | 0.01 | 0.08 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.36 | 0.04 | 0.31 | 0.03 | 0.20 | 0.03 | 0.14 | 0.01 | 0.39 | 0.03 | 0.24 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.05 | 0.01 | 0.14 | 0.01 | 0.24 | 0.02 |
| CYP7A1 | ENSG00000167910 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.04 | 0.03 | 0.07 | 0.02 | 0.00 | 0.00 | 0.01 | 0.08 | 0.13 | 0.01 | 0.12 | 0.02 | 0.04 | 0.01 | 0.07 | 0.02 | 0.06 | 0.02 | 0.07 | 0.00 | 0.10 | 0.02 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.18 | 0.01 | 0.38 | 0.03 | 0.03 | 0.01 | 0.08 | 0.00 | 0.59 | 0.09 | 0.13 | 0.03 | 0.17 | 0.00 | 0.01 | 0.00 | 0.00 | 0.11 | 0.00 | 0.00 | 0.00 | 0.01 | 0.22 | 0.00 | 0.06 | 0.01 |
| ITFG3 | ENSG00000167930 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.06 | 0.05 | 0.05 | 0.09 | 0.03 | 0.03 | 0.02 | 0.14 | 0.05 | 0.09 | 0.03 | 0.04 | 0.03 | 0.03 | 0.01 | 0.03 | 0.03 | 0.06 | 0.00 | 0.05 | 0.14 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.03 | 0.14 | 0.22 | 0.10 | 0.06 | 0.09 | 0.05 | 0.14 | 0.19 | 0.08 | 0.09 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| SOST | ENSG00000167941 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.04 | 0.03 | 0.01 | 0.00 | 0.02 | 0.04 | 0.06 | 0.01 | 0.04 | 0.06 | 0.02 | 0.02 | 0.11 | 0.01 | 0.10 | 0.02 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.03 | 0.02 | 0.01 | 0.07 | 0.14 | 0.00 | 0.09 | 0.00 | 0.00 | 0.04 | 0.11 | 0.03 | 0.14 | 0.04 | 0.03 | 0.03 | 0.07 | 0.12 | 0.17 | 0.06 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.04 |
| DNASE1L2 | ENSG00000167968 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.04 | 0.03 | 0.07 | 0.03 | 0.03 | 0.02 | 0.10 | 0.03 | 0.08 | 0.03 | 0.03 | 0.01 | 0.03 | 0.02 | 0.02 | 0.04 | 0.03 | 0.00 | 0.05 | 0.17 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 | 0.10 | 0.17 | 0.11 | 0.03 | 0.06 | 0.02 | 0.30 | 0.05 | 0.10 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.04 | 0.02 |
| SLC22A11 | ENSG00000168065 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.03 | 0.01 | 0.11 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.05 | 0.03 | 0.07 | 0.02 | 0.20 | 0.02 | 0.11 | 0.05 | 0.03 | 0.03 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.08 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.08 | 0.17 | 0.05 | 0.11 | 0.01 | 0.07 | 0.02 | 0.23 | 0.04 | 0.08 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.05 |
| PBK | ENSG00000168078 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.18 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.06 | 0.01 | 0.08 | 0.01 | 0.04 | 0.06 | 0.10 | 0.01 | 0.04 | 0.01 | 0.08 | 0.00 | 0.18 | 0.00 | 0.04 | 0.01 | 0.10 | 0.00 | 0.08 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.13 | 0.04 | 0.36 | 0.00 | 0.03 | 0.01 | 0.11 | 0.09 | 0.14 | 0.07 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.05 |
| SCARA5 | ENSG00000168079 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.17 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.06 | 0.01 | 0.08 | 0.01 | 0.04 | 0.08 | 0.09 | 0.02 | 0.04 | 0.01 | 0.08 | 0.00 | 0.18 | 0.00 | 0.05 | 0.01 | 0.10 | 0.00 | 0.08 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.14 | 0.03 | 0.36 | 0.00 | 0.02 | 0.01 | 0.10 | 0.12 | 0.14 | 0.08 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.05 |
| PNOC | ENSG00000168081 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.14 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.06 | 0.00 | 0.08 | 0.01 | 0.03 | 0.08 | 0.10 | 0.02 | 0.04 | 0.02 | 0.08 | 0.00 | 0.18 | 0.02 | 0.04 | 0.02 | 0.10 | 0.00 | 0.08 | 0.02 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.13 | 0.03 | 0.34 | 0.00 | 0.02 | 0.01 | 0.08 | 0.01 | 0.14 | 0.04 | 0.08 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 | 0.05 |
| OR1F1 | ENSG00000168124 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.18 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.03 | 0.03 | 0.10 | 0.04 | 0.02 | 0.02 | 0.08 | 0.03 | 0.08 | 0.04 | 0.03 | 0.04 | 0.03 | 0.02 | 0.02 | 0.03 | 0.02 | 0.05 | 0.05 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.09 | 0.19 | 0.10 | 0.02 | 0.04 | 0.05 | 0.07 | 0.05 | 0.09 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.05 | 0.02 |
| OR2W6P | ENSG00000168126 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.19 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 | 0.06 | 0.02 | 0.06 | 0.06 | 0.02 | 0.04 | 0.09 | 0.11 | 0.07 | 0.05 | 0.04 | 0.02 | 0.06 | 0.02 | 0.02 | 0.03 | 0.09 | 0.02 | 0.06 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.33 | 0.06 | 0.08 | 0.04 | 0.04 | 0.01 | 0.26 | 0.02 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.14 | 0.01 |
| OR2B2 | ENSG00000168131 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.19 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 | 0.06 | 0.02 | 0.06 | 0.05 | 0.02 | 0.04 | 0.09 | 0.12 | 0.08 | 0.05 | 0.04 | 0.02 | 0.06 | 0.02 | 0.02 | 0.03 | 0.09 | 0.02 | 0.06 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.03 | 0.32 | 0.06 | 0.08 | 0.04 | 0.04 | 0.01 | 0.26 | 0.02 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.13 | 0.00 | 0.14 | 0.01 |
| OR2C1 | ENSG00000168158 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.18 | 0.00 | 0.00 | 0.04 | 0.02 | 0.04 | 0.03 | 0.03 | 0.09 | 0.04 | 0.02 | 0.02 | 0.08 | 0.02 | 0.08 | 0.03 | 0.03 | 0.03 | 0.03 | 0.02 | 0.02 | 0.03 | 0.02 | 0.05 | 0.05 | 0.11 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.08 | 0.21 | 0.10 | 0.02 | 0.03 | 0.06 | 0.05 | 0.05 | 0.08 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.06 | 0.02 |
| PTGDR | ENSG00000168229 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.12 | 0.01 | 0.06 | 0.04 | 0.07 | 0.01 | 0.13 | 0.01 | 0.06 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.02 | 0.01 | 0.03 | 0.05 | 0.05 | 0.06 | 0.04 | 0.05 | 0.01 | 0.01 | 0.00 | 0.00 | 0.10 | 0.02 | 0.09 | 0.13 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.03 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 |
| KCNV2 | ENSG00000168263 | 0.02 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.06 | 0.13 | 0.08 | 0.01 | 0.01 | 0.04 | 0.09 | 0.05 | 0.12 | 0.12 | 0.11 | 0.17 | 0.07 | 0.09 | 0.15 | 0.13 | 0.13 | 0.02 | 0.02 | 0.04 | 0.04 | 0.01 | 0.08 | 0.07 | 0.03 | 0.03 | 0.01 | 0.15 | 0.03 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.06 | 0.21 | 0.18 | 0.14 | 0.06 | 0.08 | 0.03 | 0.05 | 0.24 | 0.15 | 0.15 | 0.02 | 0.10 | 0.00 | 0.00 | 0.08 | 0.02 | 0.01 | 0.08 | 0.01 | 0.16 | 0.00 | 0.00 | 0.05 | 0.10 |
| CX3CR1 | ENSG00000168329 | 0.00 | 0.18 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.01 | 0.13 | 0.05 | 0.00 | 0.02 | 0.02 | 0.32 | 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 | 0.09 | 0.12 | 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 |
| TAP1 | ENSG00000168394 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.08 | 0.02 | 0.05 | 0.05 | 0.03 | 0.04 | 0.15 | 0.05 | 0.09 | 0.04 | 0.03 | 0.02 | 0.06 | 0.02 | 0.04 | 0.01 | 0.08 | 0.01 | 0.05 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.28 | 0.06 | 0.09 | 0.01 | 0.05 | 0.01 | 0.05 | 0.03 | 0.05 | 0.07 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.17 | 0.01 | 0.01 | 0.01 | 0.01 | 0.11 | 0.00 | 0.11 | 0.01 |
| ING5 | ENSG00000168395 | 0.01 | 0.08 | 0.04 | 0.05 | 0.00 | 0.10 | 0.02 | 0.04 | 0.00 | 0.32 | 0.00 | 0.01 | 0.00 | 0.07 | 0.05 | 0.05 | 0.03 | 0.20 | 0.02 | 0.18 | 0.04 | 0.18 | 0.03 | 0.10 | 0.02 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.09 | 0.05 | 0.01 | 0.05 | 0.11 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.12 | 0.22 | 0.30 | 0.02 | 0.38 | 0.03 | 0.08 | 0.13 | 0.09 | 0.05 | 0.53 | 0.03 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.00 | 0.04 | 0.04 | 0.05 | 0.01 | 0.14 |
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