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 |
| IL17RC | ENSG00000163702 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.06 | 0.42 | 0.02 | 0.00 | 0.03 | 0.03 | 0.06 | 0.05 | 0.04 | 0.02 | 0.04 | 0.03 | 0.02 | 0.08 | 0.05 | 0.07 | 0.06 | 0.00 | 0.04 | 0.01 | 0.06 | 0.01 | 0.02 | 0.08 | 0.01 | 0.00 | 0.18 | 0.13 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.13 | 0.02 | 0.17 | 0.22 | 0.02 | 0.02 | 0.05 | 0.03 | 0.11 | 0.14 | 0.21 | 0.05 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.04 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 |
| TDRD7 | ENSG00000196116 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.04 | 0.04 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.03 | 0.04 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.05 | 0.15 | 0.02 | 0.02 | 0.02 | 0.04 | 0.00 | 0.15 | 0.08 | 0.04 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 |
| SLC35A5 | ENSG00000138459 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.06 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.13 | 0.03 | 0.05 | 0.01 | 0.09 | 0.05 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.01 | 0.10 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.06 | 0.02 | 0.38 | 0.04 | 0.05 | 0.01 | 0.04 | 0.01 | 0.03 | 0.08 | 0.13 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.02 | 0.04 |
| CDK17 | ENSG00000059758 | 0.01 | 0.01 | 0.01 | 0.00 | 0.06 | 0.03 | 0.05 | 0.01 | 0.08 | 0.04 | 0.00 | 0.00 | 0.02 | 0.03 | 0.02 | 0.05 | 0.03 | 0.03 | 0.02 | 0.03 | 0.06 | 0.06 | 0.05 | 0.03 | 0.00 | 0.02 | 0.01 | 0.04 | 0.01 | 0.06 | 0.03 | 0.03 | 0.00 | 0.17 | 0.01 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.07 | 0.06 | 0.06 | 0.22 | 0.01 | 0.02 | 0.02 | 0.03 | 0.01 | 0.09 | 0.68 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.03 | 0.08 |
| CACNG3 | ENSG00000006116 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.18 | 0.03 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.01 | 0.11 | 0.01 | 0.04 | 0.02 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.07 | 0.05 | 0.01 | 0.02 | 0.05 | 0.01 | 0.17 | 0.03 | 0.05 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.01 | 0.02 |
| VRK3 | ENSG00000105053 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.07 | 0.06 | 0.10 | 0.03 | 0.02 | 0.07 | 0.03 | 0.07 | 0.03 | 0.01 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.03 | 0.03 | 0.00 | 0.07 | 0.23 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.10 | 0.04 | 0.06 | 0.32 | 0.05 | 0.07 | 0.04 | 0.06 | 0.11 | 0.15 | 0.02 | 0.18 | 0.00 | 0.04 | 0.01 | 0.00 | 0.10 | 0.06 | 0.00 | 0.14 | 0.02 | 0.13 | 0.00 | 0.00 | 0.02 | 0.02 |
| ATP2C1 | ENSG00000017260 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.04 | 0.02 | 0.00 | 0.01 | 0.00 | 0.03 | 0.04 | 0.02 | 0.15 | 0.01 | 0.09 | 0.00 | 0.16 | 0.03 | 0.06 | 0.02 | 0.01 | 0.00 | 0.02 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.06 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.03 | 0.30 | 0.04 | 0.11 | 0.01 | 0.07 | 0.00 | 0.18 | 0.03 | 0.04 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.05 | 0.00 | 0.00 | 0.01 | 0.04 |
| SLC25A1 | ENSG00000100075 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.17 | 0.06 | 0.03 | 0.01 | 0.08 | 0.05 | 0.07 | 0.03 | 0.17 | 0.07 | 0.10 | 0.03 | 0.08 | 0.07 | 0.05 | 0.04 | 0.02 | 0.01 | 0.06 | 0.03 | 0.00 | 0.02 | 0.02 | 0.03 | 0.08 | 0.10 | 0.10 | 0.14 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.05 | 0.19 | 0.07 | 0.05 | 0.01 | 0.06 | 0.06 | 0.42 | 0.04 | 0.14 | 0.07 | 0.13 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.13 | 0.03 |
| CASP7 | ENSG00000165806 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.05 | 0.02 | 0.09 | 0.00 | 0.02 | 0.01 | 0.17 | 0.06 | 0.03 | 0.04 | 0.06 | 0.01 | 0.03 | 0.04 | 0.06 | 0.08 | 0.06 | 0.01 | 0.07 | 0.02 | 0.06 | 0.01 | 0.01 | 0.02 | 0.10 | 0.11 | 0.21 | 0.11 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.10 | 0.19 | 0.22 | 0.01 | 0.07 | 0.03 | 0.07 | 0.07 | 0.05 | 0.04 | 0.05 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.05 |
| ICK | ENSG00000112144 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.10 | 0.05 | 0.00 | 0.00 | 0.00 | 0.03 | 0.07 | 0.01 | 0.21 | 0.04 | 0.11 | 0.02 | 0.25 | 0.04 | 0.18 | 0.02 | 0.02 | 0.01 | 0.09 | 0.02 | 0.01 | 0.00 | 0.08 | 0.00 | 0.00 | 0.05 | 0.08 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.02 | 0.19 | 0.07 | 0.09 | 0.04 | 0.04 | 0.01 | 0.17 | 0.03 | 0.09 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.05 | 0.02 |
| PARL | ENSG00000175193 | 0.05 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.03 | 0.17 | 0.01 | 0.00 | 0.00 | 0.00 | 0.09 | 0.15 | 0.05 | 1.90 | 0.00 | 0.68 | 0.00 | 0.67 | 0.02 | 0.24 | 0.01 | 0.04 | 0.00 | 0.06 | 0.03 | 0.03 | 0.01 | 0.11 | 0.02 | 0.12 | 0.01 | 0.12 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 | 0.19 | 0.02 | 1.12 | 0.02 | 0.63 | 0.00 | 0.34 | 0.01 | 0.76 | 0.09 | 0.11 | 0.10 | 0.22 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.07 | 0.00 | 0.20 | 0.02 | 0.00 | 0.00 | 0.02 | 0.05 |
| PIK3R2 | ENSG00000105647 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 | 0.03 | 0.02 | 0.09 | 0.02 | 0.05 | 0.02 | 0.11 | 0.01 | 0.04 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.02 | 0.09 | 0.03 | 0.06 | 0.03 | 0.13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.52 | 0.04 | 0.02 | 0.02 | 0.18 | 0.03 | 0.33 | 0.07 | 0.07 | 0.02 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.01 |
| LYG2 | ENSG00000185674 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.13 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.01 | 0.13 | 0.02 | 0.07 | 0.02 | 0.19 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.17 | 0.06 | 0.03 | 0.02 | 0.05 | 0.01 | 0.17 | 0.00 | 0.15 | 0.04 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 |
| ADCK4 | ENSG00000123815 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.19 | 0.02 | 0.00 | 0.00 | 0.08 | 0.02 | 0.15 | 0.04 | 0.34 | 0.06 | 0.04 | 0.02 | 0.03 | 0.05 | 0.08 | 0.03 | 0.05 | 0.01 | 0.01 | 0.02 | 0.14 | 0.01 | 0.08 | 0.02 | 0.12 | 0.01 | 0.09 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.08 | 0.04 | 0.38 | 0.24 | 0.10 | 0.04 | 0.11 | 0.04 | 0.88 | 0.11 | 0.22 | 0.12 | 0.00 | 0.03 | 0.01 | 0.00 | 0.05 | 0.00 | 0.02 | 0.07 | 0.02 | 0.07 | 0.00 | 0.00 | 0.02 | 0.02 |
| NPFFR1 | ENSG00000148734 | 0.00 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.03 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.07 | 0.03 | 0.03 | 0.02 | 0.05 | 0.05 | 0.10 | 0.02 | 0.03 | 0.03 | 0.05 | 0.03 | 0.01 | 0.00 | 0.02 | 0.02 | 0.25 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.07 | 0.03 | 0.13 | 0.11 | 0.01 | 0.01 | 0.07 | 0.03 | 0.14 | 0.05 | 0.02 | 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 |
| HTT | ENSG00000197386 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.08 | 0.04 | 0.00 | 0.02 | 0.00 | 0.03 | 0.04 | 0.04 | 0.04 | 0.04 | 0.03 | 0.06 | 0.04 | 0.08 | 0.06 | 0.06 | 0.02 | 0.03 | 0.04 | 0.03 | 0.01 | 0.02 | 0.04 | 0.07 | 0.00 | 0.01 | 0.08 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.03 | 0.05 | 0.31 | 0.08 | 0.02 | 0.05 | 0.07 | 0.05 | 0.15 | 0.00 | 0.12 | 0.04 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.05 | 0.05 |
| PRDM4 | ENSG00000110851 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.03 | 0.07 | 0.04 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.05 | 0.02 | 0.04 | 0.02 | 0.03 | 0.06 | 0.04 | 0.05 | 0.01 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.06 | 0.02 | 0.04 | 0.00 | 0.22 | 0.10 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.04 | 0.07 | 0.09 | 0.21 | 0.02 | 0.01 | 0.01 | 0.05 | 0.02 | 0.11 | 0.16 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.10 | 0.00 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.02 | 0.07 |
| CYP20A1 | ENSG00000119004 | 0.03 | 0.03 | 0.04 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.03 | 0.13 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.02 | 0.14 | 0.08 | 0.09 | 0.12 | 0.11 | 0.05 | 0.06 | 0.03 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.08 | 0.02 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.03 | 0.24 | 0.11 | 0.05 | 0.23 | 0.06 | 0.03 | 0.08 | 0.05 | 0.05 | 0.13 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 |
| STK38 | ENSG00000112079 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.10 | 0.04 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.01 | 0.05 | 0.05 | 0.02 | 0.03 | 0.18 | 0.03 | 0.07 | 0.02 | 0.02 | 0.01 | 0.07 | 0.01 | 0.01 | 0.01 | 0.07 | 0.04 | 0.05 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.30 | 0.04 | 0.08 | 0.00 | 0.06 | 0.01 | 0.30 | 0.03 | 0.03 | 0.07 | 0.05 | 0.01 | 0.00 | 0.00 | 0.08 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.10 | 0.00 | 0.08 | 0.01 |
| STK40 | ENSG00000196182 | 0.00 | 0.03 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.06 | 0.00 | 0.00 | 0.08 | 0.05 | 0.07 | 0.04 | 0.05 | 0.04 | 0.05 | 0.02 | 0.08 | 0.05 | 0.06 | 0.04 | 0.02 | 0.04 | 0.01 | 0.05 | 0.02 | 0.01 | 0.01 | 0.13 | 0.00 | 0.33 | 0.02 | 0.03 | 0.03 | 0.07 | 0.00 | 0.00 | 0.06 | 0.06 | 0.56 | 0.11 | 0.05 | 0.02 | 0.09 | 0.04 | 0.20 | 0.04 | 0.10 | 0.04 | 0.06 | 0.03 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.04 | 0.03 | 0.00 | 0.10 | 0.04 | 0.03 |
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