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 |
| GLRA4 | ENSG00000188828 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.03 | 0.11 | 0.01 | 0.03 | 0.01 | 0.08 | 0.03 | 0.05 | 0.01 | 0.02 | 0.01 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.03 | 0.05 | 0.05 | 0.04 | 0.02 | 0.02 | 0.02 | 0.01 | 0.02 | 0.17 | 0.10 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 |
| ASTL | ENSG00000188886 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.01 | 0.15 | 0.01 | 0.10 | 0.01 | 0.13 | 0.01 | 0.07 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.18 | 0.05 | 0.03 | 0.01 | 0.06 | 0.01 | 0.32 | 0.00 | 0.19 | 0.01 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 |
| NYX | ENSG00000188937 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.01 | 0.02 | 0.04 | 0.00 | 0.03 | 0.05 | 0.06 | 0.04 | 0.01 | 0.00 | 0.00 | 0.03 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.09 | 0.09 | 0.00 | 0.03 | 0.01 | 0.02 | 0.13 | 0.06 | 0.13 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 |
| SLC15A5 | ENSG00000188991 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.09 | 0.02 | 0.04 | 0.01 | 0.00 | 0.00 | 0.06 | 0.06 | 0.09 | 0.12 | 0.02 | 0.05 | 0.02 | 0.08 | 0.05 | 0.04 | 0.06 | 0.02 | 0.02 | 0.05 | 0.05 | 0.02 | 0.07 | 0.00 | 0.03 | 0.14 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.07 | 0.06 | 0.23 | 0.11 | 0.01 | 0.03 | 0.03 | 0.02 | 0.21 | 0.03 | 0.13 | 0.13 | 0.58 | 0.00 | 0.00 | 0.02 | 0.00 | 0.04 | 0.03 | 0.02 | 0.02 | 0.05 | 0.00 | 0.01 | 0.02 | 0.04 |
| SBSN | ENSG00000189001 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.01 | 0.01 | 0.19 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.26 | 0.00 | 0.43 | 0.03 | 0.08 | 0.01 | 0.22 | 0.03 | 0.08 | 0.04 | 0.05 | 0.00 | 0.04 | 0.00 | 0.10 | 0.00 | 0.05 | 0.02 | 0.13 | 0.01 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.14 | 0.02 | 0.64 | 0.05 | 0.22 | 0.02 | 0.18 | 0.02 | 1.50 | 0.01 | 0.29 | 0.05 | 0.01 | 0.03 | 0.00 | 0.01 | 0.08 | 0.00 | 0.02 | 0.01 | 0.03 | 0.02 | 0.00 | 0.00 | 0.04 | 0.01 |
| KIR2DL4 | ENSG00000189013 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.20 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.05 | 0.09 | 0.09 | 0.05 | 0.02 | 0.12 | 0.03 | 0.10 | 0.03 | 0.02 | 0.02 | 0.01 | 0.04 | 0.03 | 0.04 | 0.06 | 0.02 | 0.02 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.15 | 0.03 | 0.17 | 0.26 | 0.12 | 0.06 | 0.06 | 0.05 | 0.25 | 0.10 | 0.05 | 0.18 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.18 | 0.02 | 0.12 | 0.00 | 0.00 | 0.04 | 0.04 |
| DUSP21 | ENSG00000189037 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.01 | 0.05 | 0.05 | 0.01 | 0.04 | 0.09 | 0.06 | 0.03 | 0.02 | 0.00 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.01 | 0.13 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.17 | 0.08 | 0.01 | 0.04 | 0.06 | 0.02 | 0.23 | 0.05 | 0.11 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 |
| NDUFA4 | ENSG00000189043 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.14 | 0.01 | 0.00 | 0.01 | 0.08 | 0.01 | 0.08 | 0.01 | 0.12 | 0.01 | 0.08 | 0.01 | 0.15 | 0.03 | 0.09 | 0.01 | 0.04 | 0.00 | 0.04 | 0.00 | 0.01 | 0.00 | 0.06 | 0.01 | 0.01 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.04 | 0.10 | 0.35 | 0.02 | 0.02 | 0.06 | 0.05 | 0.08 | 0.03 | 0.16 | 0.05 | 0.10 | 0.00 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.12 | 0.00 |
| APOD | ENSG00000189058 | 0.05 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.03 | 0.06 | 0.18 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.15 | 0.06 | 1.36 | 0.01 | 0.58 | 0.00 | 0.79 | 0.04 | 0.24 | 0.02 | 0.05 | 0.01 | 0.06 | 0.02 | 0.03 | 0.01 | 0.12 | 0.03 | 0.12 | 0.03 | 0.10 | 0.03 | 0.00 | 0.10 | 0.00 | 0.00 | 0.21 | 0.03 | 1.02 | 0.09 | 0.65 | 0.00 | 0.38 | 0.01 | 0.77 | 0.15 | 0.11 | 0.14 | 0.16 | 0.03 | 0.00 | 0.00 | 0.35 | 0.04 | 0.02 | 0.07 | 0.06 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| H1F0 | ENSG00000189060 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.12 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.07 | 0.03 | 0.09 | 0.02 | 0.01 | 0.01 | 0.04 | 0.02 | 0.04 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.08 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.03 | 0.02 | 0.14 | 0.10 | 0.04 | 0.01 | 0.10 | 0.01 | 0.40 | 0.10 | 0.06 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.04 | 0.02 | 0.00 | 0.14 | 0.01 |
| PRSS48 | ENSG00000189099 | 0.01 | 0.02 | 0.00 | 0.01 | 0.06 | 0.00 | 0.03 | 0.01 | 0.07 | 0.10 | 0.00 | 0.00 | 0.00 | 0.03 | 0.05 | 0.03 | 0.01 | 0.11 | 0.01 | 0.08 | 0.08 | 0.08 | 0.06 | 0.09 | 0.02 | 0.03 | 0.02 | 0.04 | 0.05 | 0.03 | 0.06 | 0.05 | 0.00 | 0.12 | 0.10 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.06 | 0.06 | 0.09 | 0.24 | 0.03 | 0.07 | 0.03 | 0.04 | 0.10 | 0.04 | 0.11 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.03 | 0.06 | 0.01 | 0.08 | 0.00 | 0.03 | 0.00 | 0.00 | 0.03 | 0.04 |
| S100A13 | ENSG00000189171 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.06 | 0.00 | 0.43 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.39 | 0.00 | 0.27 | 0.00 | 0.05 | 0.01 | 0.24 | 0.01 | 0.19 | 0.00 | 0.02 | 0.00 | 0.17 | 0.00 | 0.06 | 0.00 | 0.36 | 0.00 | 0.49 | 0.01 | 0.14 | 0.02 | 0.13 | 0.00 | 0.00 | 0.00 | 0.31 | 0.00 | 0.60 | 0.02 | 0.19 | 0.00 | 0.22 | 0.00 | 0.61 | 0.00 | 0.46 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.20 | 0.04 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.20 | 0.00 |
| OR14I1 | ENSG00000189181 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.04 | 0.14 | 0.04 | 0.02 | 0.02 | 0.08 | 0.05 | 0.13 | 0.01 | 0.17 | 0.03 | 0.10 | 0.02 | 0.27 | 0.04 | 0.13 | 0.01 | 0.04 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.20 | 0.02 | 0.23 | 0.02 | 0.10 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.29 | 0.02 | 0.48 | 0.12 | 0.13 | 0.01 | 0.12 | 0.02 | 0.32 | 0.00 | 0.09 | 0.24 | 0.06 | 0.02 | 0.01 | 0.00 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.24 | 0.02 |
| CXCL17 | ENSG00000189377 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.08 | 0.13 | 0.03 | 0.00 | 0.00 | 0.14 | 0.05 | 0.10 | 0.05 | 0.13 | 0.07 | 0.01 | 0.02 | 0.03 | 0.07 | 0.04 | 0.03 | 0.02 | 0.02 | 0.02 | 0.03 | 0.02 | 0.03 | 0.06 | 0.03 | 0.12 | 0.01 | 0.17 | 0.04 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.05 | 0.19 | 0.28 | 0.12 | 0.05 | 0.05 | 0.04 | 0.09 | 0.17 | 0.18 | 0.12 | 0.00 | 0.04 | 0.01 | 0.00 | 0.05 | 0.06 | 0.01 | 0.11 | 0.03 | 0.09 | 0.00 | 0.00 | 0.03 | 0.03 |
| HMGB1 | ENSG00000189403 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.09 | 0.17 | 0.05 | 0.00 | 0.02 | 0.00 | 0.18 | 0.02 | 0.08 | 0.04 | 0.11 | 0.02 | 0.14 | 0.12 | 0.06 | 0.16 | 0.03 | 0.16 | 0.00 | 0.28 | 0.02 | 0.01 | 0.01 | 0.03 | 0.15 | 0.00 | 0.14 | 0.00 | 0.09 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.06 | 0.07 | 0.17 | 0.02 | 0.16 | 0.01 | 0.05 | 0.01 | 0.15 | 0.10 | 0.30 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.05 | 0.01 | 0.07 | 0.00 | 0.00 | 0.09 | 0.02 |
| MMP23B | ENSG00000189409 | 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 |
| NCR1 | ENSG00000189430 | 0.01 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.03 | 0.00 | 0.20 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.05 | 0.05 | 0.09 | 0.09 | 0.05 | 0.02 | 0.12 | 0.03 | 0.11 | 0.03 | 0.02 | 0.03 | 0.01 | 0.04 | 0.03 | 0.04 | 0.06 | 0.02 | 0.02 | 0.07 | 0.21 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 | 0.15 | 0.03 | 0.17 | 0.26 | 0.12 | 0.06 | 0.06 | 0.05 | 0.25 | 0.10 | 0.04 | 0.17 | 0.00 | 0.06 | 0.01 | 0.00 | 0.13 | 0.03 | 0.01 | 0.18 | 0.02 | 0.12 | 0.00 | 0.00 | 0.04 | 0.04 |
| OR2L13 | ENSG00000196071 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.04 | 0.14 | 0.04 | 0.02 | 0.02 | 0.08 | 0.05 | 0.13 | 0.01 | 0.17 | 0.03 | 0.10 | 0.02 | 0.27 | 0.04 | 0.13 | 0.01 | 0.04 | 0.02 | 0.08 | 0.01 | 0.02 | 0.01 | 0.20 | 0.02 | 0.23 | 0.02 | 0.10 | 0.07 | 0.00 | 0.04 | 0.00 | 0.00 | 0.29 | 0.02 | 0.48 | 0.12 | 0.13 | 0.01 | 0.12 | 0.02 | 0.32 | 0.00 | 0.09 | 0.24 | 0.06 | 0.02 | 0.01 | 0.00 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.04 | 0.15 | 0.03 | 0.24 | 0.02 |
| OR5K4 | ENSG00000196098 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.04 | 0.06 | 0.02 | 0.17 | 0.03 | 0.06 | 0.01 | 0.11 | 0.03 | 0.05 | 0.03 | 0.00 | 0.01 | 0.03 | 0.01 | 0.00 | 0.01 | 0.02 | 0.02 | 0.00 | 0.12 | 0.10 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.05 | 0.02 | 0.23 | 0.04 | 0.05 | 0.02 | 0.04 | 0.00 | 0.18 | 0.08 | 0.07 | 0.06 | 0.04 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 |
| OR6M1 | ENSG00000196099 | 0.00 | 0.01 | 0.00 | 0.05 | 0.02 | 0.02 | 0.02 | 0.06 | 0.03 | 0.09 | 0.00 | 0.00 | 0.13 | 0.06 | 0.05 | 0.09 | 0.05 | 0.10 | 0.04 | 0.14 | 0.05 | 0.14 | 0.05 | 0.08 | 0.01 | 0.01 | 0.01 | 0.03 | 0.01 | 0.02 | 0.00 | 0.09 | 0.00 | 0.19 | 0.00 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.22 | 0.17 | 0.17 | 0.04 | 0.31 | 0.04 | 0.07 | 0.05 | 0.17 | 0.03 | 0.23 | 0.00 | 0.24 | 0.03 | 0.00 | 0.13 | 0.02 | 0.06 | 0.01 | 0.01 | 0.01 | 0.00 | 0.10 | 0.00 | 0.26 |
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