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 |
| IFNAR1 | ENSG00000142166 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.03 | 0.03 | 0.05 | 0.02 | 0.03 | 0.00 | 0.06 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.03 | 0.15 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.11 | 0.04 | 0.02 | 0.01 | 0.03 | 0.00 | 0.04 | 0.03 | 0.04 | 0.04 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 |
| CSNK1G1 | ENSG00000169118 | 0.00 | 0.00 | 0.01 | 0.00 | 0.14 | 0.00 | 0.01 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.03 | 0.04 | 0.05 | 0.03 | 0.02 | 0.02 | 0.03 | 0.03 | 0.03 | 0.05 | 0.02 | 0.02 | 0.02 | 0.04 | 0.02 | 0.01 | 0.02 | 0.01 | 0.00 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.11 | 0.12 | 0.05 | 0.01 | 0.01 | 0.06 | 0.11 | 0.21 | 0.10 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 |
| TDRD3 | ENSG00000083544 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.30 | 0.06 | 0.18 | 0.00 | 0.00 | 0.00 | 0.09 | 0.05 | 0.04 | 0.04 | 0.11 | 0.03 | 0.09 | 0.06 | 0.10 | 0.08 | 0.06 | 0.07 | 0.01 | 0.13 | 0.01 | 0.01 | 0.00 | 0.03 | 0.21 | 0.00 | 0.07 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.09 | 0.09 | 0.16 | 0.04 | 0.14 | 0.02 | 0.03 | 0.05 | 0.17 | 0.05 | 0.26 | 0.02 | 0.01 | 0.00 | 0.00 | 0.03 | 0.06 | 0.00 | 0.08 | 0.01 | 0.14 | 0.00 | 0.00 | 0.05 | 0.04 |
| SLC9B1 | ENSG00000164037 | 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 | 0.02 | 0.03 | 0.03 | 0.05 | 0.01 | 0.02 | 0.02 | 0.06 | 0.02 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.00 | 0.01 | 0.01 | 0.13 | 0.00 | 0.03 | 0.04 | 0.09 | 0.04 | 0.01 | 0.00 | 0.00 | 0.05 | 0.05 | 0.03 | 0.31 | 0.01 | 0.01 | 0.01 | 0.04 | 0.00 | 0.11 | 0.02 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 |
| ROCK1 | ENSG00000067900 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.06 | 0.02 | 0.07 | 0.04 | 0.21 | 0.02 | 0.11 | 0.01 | 0.02 | 0.00 | 0.06 | 0.01 | 0.10 | 0.01 | 0.01 | 0.00 | 0.04 | 0.05 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.07 | 0.04 | 0.00 | 0.00 | 0.03 | 0.01 | 0.06 | 0.02 | 0.11 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| TRPC4 | ENSG00000133107 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.29 | 0.09 | 0.17 | 0.00 | 0.02 | 0.02 | 0.18 | 0.02 | 0.08 | 0.03 | 0.10 | 0.02 | 0.16 | 0.06 | 0.07 | 0.14 | 0.03 | 0.13 | 0.02 | 0.17 | 0.03 | 0.01 | 0.01 | 0.01 | 0.21 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.04 | 0.00 | 0.01 | 0.05 | 0.12 | 0.06 | 0.22 | 0.01 | 0.22 | 0.00 | 0.05 | 0.07 | 0.23 | 0.09 | 0.26 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.06 | 0.01 | 0.11 | 0.00 | 0.00 | 0.04 | 0.03 |
| ERP44 | ENSG00000023318 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.05 | 0.00 | 0.01 | 0.02 | 0.06 | 0.02 | 0.04 | 0.05 | 0.03 | 0.04 | 0.01 | 0.07 | 0.01 | 0.02 | 0.04 | 0.01 | 0.01 | 0.04 | 0.03 | 0.00 | 0.01 | 0.01 | 0.06 | 0.00 | 0.08 | 0.05 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.06 | 0.06 | 0.16 | 0.02 | 0.05 | 0.01 | 0.04 | 0.00 | 0.15 | 0.10 | 0.03 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 |
| PSEN1 | ENSG00000080815 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.05 | 0.00 | 0.01 | 0.00 | 0.06 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.01 | 0.05 | 0.03 | 0.01 | 0.04 | 0.01 | 0.03 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.09 | 0.00 | 0.33 | 0.00 | 0.05 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.10 | 0.08 | 0.22 | 0.06 | 0.02 | 0.04 | 0.02 | 0.15 | 0.04 | 0.05 | 0.13 | 0.03 | 0.01 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.03 | 0.08 | 0.03 | 0.00 | 0.01 | 0.05 |
| SLC29A3 | ENSG00000198246 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.03 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.09 | 0.03 | 0.04 | 0.02 | 0.06 | 0.02 | 0.13 | 0.02 | 0.02 | 0.03 | 0.04 | 0.03 | 0.01 | 0.00 | 0.03 | 0.02 | 0.25 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.08 | 0.03 | 0.15 | 0.12 | 0.00 | 0.01 | 0.07 | 0.03 | 0.11 | 0.03 | 0.02 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 |
| IFNGR1 | ENSG00000027697 | 0.00 | 0.05 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.02 | 0.07 | 0.06 | 0.00 | 0.01 | 0.00 | 0.14 | 0.03 | 0.04 | 0.05 | 0.03 | 0.07 | 0.02 | 0.13 | 0.01 | 0.12 | 0.02 | 0.02 | 0.00 | 0.04 | 0.01 | 0.03 | 0.02 | 0.01 | 0.08 | 0.00 | 0.10 | 0.10 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.06 | 0.08 | 0.28 | 0.01 | 0.04 | 0.05 | 0.02 | 0.08 | 0.03 | 0.43 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.00 | 0.04 | 0.01 | 0.11 | 0.04 | 0.09 | 0.01 | 0.14 |
| SCPEP1 | ENSG00000121064 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.19 | 0.02 | 0.01 | 0.00 | 0.12 | 0.00 | 0.10 | 0.01 | 0.13 | 0.02 | 0.04 | 0.02 | 0.14 | 0.03 | 0.05 | 0.02 | 0.02 | 0.01 | 0.06 | 0.04 | 0.01 | 0.12 | 0.11 | 0.01 | 0.12 | 0.01 | 0.08 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.44 | 0.01 | 0.18 | 0.03 | 0.08 | 0.02 | 0.08 | 0.04 | 0.23 | 0.02 | 0.14 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.01 | 0.03 | 0.00 | 0.14 | 0.00 | 0.20 | 0.02 |
| SLC22A25 | ENSG00000196600 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.02 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.12 | 0.01 | 0.05 | 0.02 | 0.07 | 0.01 | 0.14 | 0.03 | 0.14 | 0.04 | 0.04 | 0.02 | 0.01 | 0.02 | 0.03 | 0.03 | 0.00 | 0.03 | 0.02 | 0.03 | 0.02 | 0.07 | 0.05 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.08 | 0.07 | 0.15 | 0.04 | 0.07 | 0.01 | 0.07 | 0.02 | 0.28 | 0.12 | 0.08 | 0.03 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.04 |
| LIPA | ENSG00000107798 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.23 | 0.03 | 0.13 | 0.00 | 0.02 | 0.01 | 0.12 | 0.02 | 0.05 | 0.02 | 0.11 | 0.01 | 0.08 | 0.02 | 0.13 | 0.00 | 0.12 | 0.01 | 0.09 | 0.00 | 0.08 | 0.01 | 0.02 | 0.04 | 0.07 | 0.20 | 0.07 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.11 | 0.08 | 0.31 | 0.01 | 0.10 | 0.05 | 0.10 | 0.09 | 0.12 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.24 | 0.00 | 0.04 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.05 |
| SLC27A1 | ENSG00000130304 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 | 0.02 | 0.02 | 0.08 | 0.03 | 0.04 | 0.02 | 0.13 | 0.01 | 0.04 | 0.01 | 0.02 | 0.00 | 0.01 | 0.03 | 0.01 | 0.02 | 0.05 | 0.02 | 0.04 | 0.03 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.02 | 0.70 | 0.03 | 0.02 | 0.01 | 0.22 | 0.02 | 0.24 | 0.05 | 0.11 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.00 |
| TBK1 | ENSG00000183735 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.13 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.19 | 0.01 | 0.14 | 0.02 | 0.15 | 0.01 | 0.19 | 0.02 | 0.17 | 0.01 | 0.01 | 0.00 | 0.03 | 0.03 | 0.01 | 0.02 | 0.03 | 0.01 | 0.25 | 0.01 | 0.25 | 0.06 | 0.05 | 0.00 | 0.00 | 0.00 | 0.15 | 0.02 | 0.19 | 0.05 | 0.03 | 0.01 | 0.02 | 0.01 | 0.19 | 0.07 | 0.21 | 0.05 | 0.02 | 0.00 | 0.00 | 0.02 | 0.12 | 0.00 | 0.02 | 0.02 | 0.06 | 0.06 | 0.00 | 0.00 | 0.06 | 0.02 |
| PIP4K2C | ENSG00000166908 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.23 | 0.00 | 0.05 | 0.01 | 0.04 | 0.02 | 0.11 | 0.04 | 0.12 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | 0.06 | 0.01 | 0.06 | 0.01 | 0.30 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.15 | 0.05 | 0.03 | 0.00 | 0.02 | 0.01 | 0.10 | 0.05 | 0.77 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.28 | 0.02 | 0.67 | 0.04 | 0.00 | 0.00 | 0.18 | 0.03 |
| VCPKMT | ENSG00000100483 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.03 | 0.00 | 0.01 | 0.00 | 0.01 | 0.14 | 0.01 | 0.06 | 0.04 | 0.06 | 0.02 | 0.14 | 0.04 | 0.12 | 0.02 | 0.01 | 0.01 | 0.03 | 0.02 | 0.02 | 0.01 | 0.05 | 0.04 | 0.05 | 0.02 | 0.12 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.13 | 0.02 | 0.15 | 0.12 | 0.04 | 0.02 | 0.02 | 0.01 | 0.01 | 0.03 | 0.05 | 0.11 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 |
| PARP16 | ENSG00000138617 | 0.01 | 0.00 | 0.00 | 0.00 | 0.14 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.00 | 0.00 | 0.08 | 0.04 | 0.02 | 0.02 | 0.05 | 0.02 | 0.02 | 0.02 | 0.04 | 0.02 | 0.03 | 0.03 | 0.02 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.05 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.12 | 0.11 | 0.05 | 0.01 | 0.02 | 0.04 | 0.00 | 0.17 | 0.06 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.06 | 0.02 |
| CPA1 | ENSG00000091704 | 0.01 | 0.01 | 0.13 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.04 | 0.04 | 0.00 | 0.01 | 0.04 | 0.05 | 0.08 | 0.02 | 0.06 | 0.06 | 0.02 | 0.13 | 0.05 | 0.18 | 0.03 | 0.07 | 0.02 | 0.00 | 0.03 | 0.02 | 0.01 | 0.04 | 0.05 | 0.04 | 0.00 | 0.02 | 0.01 | 0.06 | 0.00 | 0.01 | 0.00 | 0.00 | 0.09 | 0.03 | 0.40 | 0.02 | 0.02 | 0.07 | 0.06 | 0.05 | 0.15 | 0.14 | 0.14 | 0.03 | 0.02 | 0.03 | 0.00 | 0.05 | 0.02 | 0.11 | 0.13 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.19 | 0.01 |
| HEXA | ENSG00000213614 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.04 | 0.01 | 0.08 | 0.01 | 0.04 | 0.02 | 0.07 | 0.02 | 0.10 | 0.02 | 0.03 | 0.00 | 0.01 | 0.03 | 0.03 | 0.01 | 0.03 | 0.02 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.23 | 0.09 | 0.10 | 0.01 | 0.04 | 0.04 | 0.17 | 0.01 | 0.06 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 |
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