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 |
| FIGF | ENSG00000165197 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.11 | 0.04 | 0.02 | 0.02 | 0.06 | 0.04 | 0.05 | 0.02 | 0.00 | 0.01 | 0.12 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.03 | 0.15 | 0.17 | 0.05 | 0.01 | 0.04 | 0.02 | 0.06 | 0.07 | 0.12 | 0.05 | 0.06 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 |
| OR1Q1 | ENSG00000165202 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.02 | 0.04 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.05 | 0.02 | 0.06 | 0.01 | 0.10 | 0.01 | 0.08 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.06 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.11 | 0.15 | 0.02 | 0.01 | 0.01 | 0.04 | 0.03 | 0.16 | 0.09 | 0.04 | 0.03 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 |
| OR1K1 | ENSG00000165204 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.02 | 0.08 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.05 | 0.02 | 0.06 | 0.01 | 0.11 | 0.01 | 0.08 | 0.01 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.04 | 0.04 | 0.06 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.12 | 0.15 | 0.02 | 0.01 | 0.02 | 0.03 | 0.03 | 0.16 | 0.09 | 0.04 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| WNK2 | ENSG00000165238 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.07 | 0.04 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.05 | 0.04 | 0.02 | 0.04 | 0.00 | 0.10 | 0.01 | 0.03 | 0.04 | 0.01 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.04 | 0.05 | 0.15 | 0.03 | 0.02 | 0.03 | 0.04 | 0.03 | 0.16 | 0.10 | 0.01 | 0.05 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 |
| NLGN4Y | ENSG00000165246 | 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 |
| FAT3 | ENSG00000165323 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.03 | 0.03 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.09 | 0.08 | 0.08 | 0.03 | 0.07 | 0.08 | 0.12 | 0.09 | 0.17 | 0.04 | 0.05 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.01 | 0.01 | 0.03 | 0.05 | 0.00 | 0.10 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.11 | 0.11 | 0.31 | 0.09 | 0.14 | 0.07 | 0.06 | 0.03 | 0.08 | 0.16 | 0.14 | 0.14 | 0.04 | 0.07 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.09 | 0.09 |
| SLC7A3 | ENSG00000165349 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.02 | 0.03 | 0.04 | 0.02 | 0.01 | 0.09 | 0.02 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.15 | 0.04 | 0.02 | 0.01 | 0.03 | 0.01 | 0.18 | 0.00 | 0.14 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 |
| GPR101 | ENSG00000165370 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.09 | 0.03 | 0.05 | 0.00 | 0.06 | 0.01 | 0.12 | 0.01 | 0.11 | 0.02 | 0.08 | 0.01 | 0.12 | 0.01 | 0.14 | 0.01 | 0.04 | 0.00 | 0.08 | 0.01 | 0.04 | 0.00 | 0.07 | 0.03 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.30 | 0.05 | 0.12 | 0.00 | 0.04 | 0.01 | 0.04 | 0.10 | 0.05 | 0.13 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.02 | 0.02 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 |
| FOLR2 | ENSG00000165457 | 0.00 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.03 | 0.00 | 0.24 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.12 | 0.01 | 0.20 | 0.03 | 0.45 | 0.03 | 0.88 | 0.02 | 0.14 | 0.03 | 0.01 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.07 | 0.02 | 0.00 | 0.02 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.28 | 0.06 | 0.45 | 0.03 | 0.11 | 0.01 | 0.07 | 0.01 | 0.16 | 0.10 | 0.11 | 0.06 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.26 | 0.01 |
| INPPL1 | ENSG00000165458 | 0.00 | 0.01 | 0.01 | 0.01 | 0.10 | 0.00 | 0.03 | 0.00 | 0.24 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.12 | 0.01 | 0.21 | 0.03 | 0.45 | 0.03 | 0.88 | 0.02 | 0.14 | 0.03 | 0.01 | 0.01 | 0.02 | 0.02 | 0.02 | 0.02 | 0.07 | 0.02 | 0.00 | 0.02 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.29 | 0.06 | 0.45 | 0.03 | 0.11 | 0.01 | 0.07 | 0.01 | 0.16 | 0.10 | 0.11 | 0.06 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.26 | 0.01 |
| MBL2 | ENSG00000165471 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.05 | 0.04 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.02 | 0.04 | 0.02 | 0.06 | 0.02 | 0.08 | 0.10 | 0.03 | 0.02 | 0.00 | 0.04 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.03 | 0.09 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.04 | 0.10 | 0.13 | 0.01 | 0.01 | 0.02 | 0.04 | 0.17 | 0.01 | 0.04 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 |
| KBTBD6 | ENSG00000165572 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.37 | 0.05 | 0.22 | 0.00 | 0.02 | 0.00 | 0.18 | 0.03 | 0.08 | 0.02 | 0.12 | 0.01 | 0.15 | 0.16 | 0.05 | 0.17 | 0.03 | 0.14 | 0.02 | 0.17 | 0.03 | 0.01 | 0.01 | 0.01 | 0.23 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.13 | 0.05 | 0.24 | 0.01 | 0.22 | 0.01 | 0.05 | 0.07 | 0.23 | 0.09 | 0.27 | 0.00 | 0.03 | 0.00 | 0.00 | 0.05 | 0.06 | 0.01 | 0.06 | 0.00 | 0.11 | 0.00 | 0.00 | 0.03 | 0.03 |
| OXGR1 | ENSG00000165621 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.17 | 0.03 | 0.00 | 0.01 | 0.01 | 0.01 | 0.10 | 0.03 | 0.09 | 0.04 | 0.10 | 0.02 | 0.06 | 0.04 | 0.14 | 0.03 | 0.09 | 0.00 | 0.13 | 0.01 | 0.04 | 0.02 | 0.25 | 0.02 | 0.06 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.14 | 0.05 | 0.22 | 0.10 | 0.17 | 0.03 | 0.04 | 0.02 | 0.37 | 0.05 | 0.24 | 0.14 | 0.01 | 0.01 | 0.00 | 0.00 | 0.04 | 0.04 | 0.02 | 0.02 | 0.03 | 0.05 | 0.05 | 0.00 | 0.06 | 0.06 |
| UCMA | ENSG00000165623 | 0.01 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.24 | 0.00 | 0.00 | 0.00 | 0.03 | 0.08 | 0.03 | 0.05 | 0.02 | 0.05 | 0.02 | 0.03 | 0.08 | 0.02 | 0.06 | 0.03 | 0.01 | 0.02 | 0.02 | 0.00 | 0.04 | 0.02 | 0.01 | 0.01 | 0.00 | 0.05 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 | 0.26 | 0.07 | 0.02 | 0.01 | 0.05 | 0.01 | 0.32 | 0.00 | 0.06 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.03 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 |
| COMTD1 | ENSG00000165644 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.07 | 0.10 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.08 | 0.05 | 0.04 | 0.03 | 0.07 | 0.03 | 0.21 | 0.04 | 0.04 | 0.02 | 0.12 | 0.04 | 0.06 | 0.00 | 0.04 | 0.04 | 0.25 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.17 | 0.03 | 0.31 | 0.10 | 0.01 | 0.01 | 0.27 | 0.02 | 0.68 | 0.00 | 0.05 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| SLC18A2 | ENSG00000165646 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.10 | 0.00 | 0.02 | 0.01 | 0.17 | 0.02 | 0.02 | 0.04 | 0.05 | 0.01 | 0.03 | 0.04 | 0.06 | 0.07 | 0.06 | 0.01 | 0.06 | 0.00 | 0.05 | 0.01 | 0.01 | 0.03 | 0.11 | 0.02 | 0.25 | 0.12 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.09 | 0.15 | 0.22 | 0.01 | 0.06 | 0.06 | 0.06 | 0.04 | 0.05 | 0.05 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.12 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.05 |
| STK32C | ENSG00000165752 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.05 | 0.08 | 0.00 | 0.03 | 0.02 | 0.11 | 0.03 | 0.05 | 0.05 | 0.07 | 0.03 | 0.04 | 0.05 | 0.09 | 0.07 | 0.07 | 0.01 | 0.06 | 0.02 | 0.04 | 0.01 | 0.01 | 0.03 | 0.10 | 0.14 | 0.17 | 0.11 | 0.06 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.12 | 0.26 | 0.22 | 0.03 | 0.05 | 0.06 | 0.06 | 0.20 | 0.04 | 0.09 | 0.14 | 0.05 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 | 0.00 | 0.14 | 0.00 | 0.09 | 0.00 | 0.00 | 0.01 | 0.07 |
| OR4K2 | ENSG00000165762 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.02 | 0.10 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.16 | 0.04 | 0.20 | 0.07 | 0.09 | 0.06 | 0.11 | 0.07 | 0.07 | 0.04 | 0.03 | 0.02 | 0.01 | 0.09 | 0.01 | 0.04 | 0.08 | 0.00 | 0.00 | 0.02 | 0.13 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.10 | 0.03 | 0.40 | 0.12 | 0.07 | 0.02 | 0.08 | 0.03 | 0.21 | 0.08 | 0.17 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.03 | 0.01 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| SLC39A2 | ENSG00000165794 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.14 | 0.03 | 0.14 | 0.08 | 0.10 | 0.06 | 0.09 | 0.07 | 0.09 | 0.04 | 0.03 | 0.02 | 0.01 | 0.08 | 0.01 | 0.05 | 0.09 | 0.00 | 0.00 | 0.02 | 0.27 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.44 | 0.10 | 0.07 | 0.01 | 0.09 | 0.03 | 0.16 | 0.08 | 0.18 | 0.08 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
| RNASE7 | ENSG00000165799 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.14 | 0.03 | 0.14 | 0.08 | 0.10 | 0.06 | 0.09 | 0.07 | 0.09 | 0.04 | 0.03 | 0.02 | 0.01 | 0.08 | 0.01 | 0.05 | 0.09 | 0.00 | 0.00 | 0.02 | 0.28 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.09 | 0.03 | 0.44 | 0.10 | 0.07 | 0.01 | 0.09 | 0.03 | 0.16 | 0.08 | 0.18 | 0.09 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.03 | 0.03 | 0.10 | 0.00 | 0.00 | 0.03 | 0.02 |
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