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 |
| ADGRE5 | ENSG00000123146 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.02 | 0.04 | 0.02 | 0.00 | 0.06 | 0.02 | 0.00 | 0.04 | 0.13 | 0.03 | 0.05 | 0.02 | 0.13 | 0.04 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.03 | 0.01 | 0.01 | 0.07 | 0.05 | 0.00 | 0.03 | 0.26 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.09 | 0.03 | 0.85 | 0.05 | 0.08 | 0.02 | 0.22 | 0.01 | 0.25 | 0.11 | 0.18 | 0.02 | 0.02 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.01 | 0.02 |
| GPR37L1 | ENSG00000170075 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.05 | 0.08 | 0.02 | 0.00 | 0.10 | 0.00 | 0.13 | 0.00 | 0.08 | 0.01 | 0.05 | 0.01 | 0.17 | 0.06 | 0.08 | 0.02 | 0.04 | 0.01 | 0.06 | 0.05 | 0.01 | 0.00 | 0.20 | 0.01 | 0.18 | 0.02 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.23 | 0.01 | 0.34 | 0.07 | 0.06 | 0.00 | 0.14 | 0.02 | 0.23 | 0.03 | 0.09 | 0.12 | 0.08 | 0.00 | 0.01 | 0.00 | 0.26 | 0.02 | 0.00 | 0.01 | 0.03 | 0.01 | 0.09 | 0.00 | 0.19 | 0.01 |
| PLA2G15 | ENSG00000103066 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.06 | 0.00 | 0.08 | 0.16 | 0.02 | 0.00 | 0.00 | 0.01 | 0.07 | 0.04 | 0.03 | 0.06 | 0.02 | 0.03 | 0.02 | 0.18 | 0.02 | 0.04 | 0.03 | 0.00 | 0.00 | 0.01 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.05 | 0.01 | 0.24 | 0.03 | 0.01 | 0.02 | 0.00 | 0.01 | 0.04 | 0.05 | 0.03 | 0.33 | 0.03 | 0.02 | 0.01 | 0.09 | 0.06 | 0.14 | 0.02 | 0.05 | 0.15 | 0.02 | 0.00 | 0.05 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.00 | 0.03 | 0.05 | 0.01 |
| CACNA1H | ENSG00000196557 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.15 | 0.00 | 0.00 | 0.04 | 0.02 | 0.05 | 0.05 | 0.04 | 0.09 | 0.03 | 0.03 | 0.03 | 0.12 | 0.04 | 0.08 | 0.03 | 0.04 | 0.03 | 0.03 | 0.01 | 0.02 | 0.04 | 0.06 | 0.00 | 0.05 | 0.18 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.02 | 0.11 | 0.19 | 0.10 | 0.05 | 0.04 | 0.04 | 0.17 | 0.21 | 0.08 | 0.05 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.05 | 0.02 |
| DPT | ENSG00000143196 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.04 | 0.47 | 0.01 | 0.02 | 0.02 | 0.10 | 0.03 | 0.15 | 0.01 | 0.25 | 0.01 | 0.04 | 0.00 | 0.22 | 0.01 | 0.15 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.25 | 0.00 | 0.30 | 0.01 | 0.00 | 0.04 | 0.05 | 0.00 | 0.00 | 0.00 | 0.21 | 0.01 | 0.33 | 0.02 | 0.14 | 0.00 | 0.10 | 0.01 | 0.34 | 0.00 | 0.36 | 0.04 | 0.09 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.14 | 0.01 |
| DDR1 | ENSG00000204580 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.16 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.09 | 0.01 | 0.07 | 0.05 | 0.04 | 0.04 | 0.20 | 0.05 | 0.15 | 0.04 | 0.04 | 0.01 | 0.07 | 0.01 | 0.03 | 0.01 | 0.12 | 0.01 | 0.08 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.03 | 0.31 | 0.06 | 0.17 | 0.01 | 0.05 | 0.01 | 0.16 | 0.03 | 0.04 | 0.05 | 0.01 | 0.01 | 0.01 | 0.00 | 0.05 | 0.14 | 0.01 | 0.00 | 0.00 | 0.01 | 0.13 | 0.00 | 0.13 | 0.01 |
| SLC24A1 | ENSG00000074621 | 0.01 | 0.00 | 0.00 | 0.00 | 0.14 | 0.00 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.00 | 0.08 | 0.00 | 0.03 | 0.02 | 0.04 | 0.03 | 0.02 | 0.02 | 0.04 | 0.02 | 0.03 | 0.03 | 0.01 | 0.01 | 0.01 | 0.02 | 0.03 | 0.02 | 0.02 | 0.01 | 0.00 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.12 | 0.12 | 0.06 | 0.01 | 0.02 | 0.04 | 0.00 | 0.17 | 0.10 | 0.01 | 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 | 0.00 |
| GRIK3 | ENSG00000163873 | 0.00 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.01 | 0.05 | 0.06 | 0.00 | 0.00 | 0.08 | 0.08 | 0.07 | 0.03 | 0.09 | 0.04 | 0.05 | 0.02 | 0.16 | 0.03 | 0.06 | 0.04 | 0.02 | 0.04 | 0.01 | 0.04 | 0.03 | 0.01 | 0.01 | 0.12 | 0.00 | 0.33 | 0.00 | 0.03 | 0.03 | 0.07 | 0.00 | 0.00 | 0.06 | 0.06 | 0.57 | 0.10 | 0.05 | 0.02 | 0.06 | 0.03 | 0.02 | 0.04 | 0.10 | 0.03 | 0.06 | 0.03 | 0.02 | 0.00 | 0.00 | 0.07 | 0.00 | 0.01 | 0.03 | 0.02 | 0.00 | 0.10 | 0.04 | 0.03 |
| HSD17B6 | ENSG00000025423 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.01 | 0.03 | 0.01 | 0.01 | 0.02 | 0.08 | 0.04 | 0.06 | 0.02 | 0.02 | 0.00 | 0.02 | 0.02 | 0.03 | 0.01 | 0.05 | 0.01 | 0.06 | 0.01 | 0.26 | 0.03 | 0.07 | 0.00 | 0.00 | 0.00 | 0.04 | 0.04 | 0.17 | 0.04 | 0.03 | 0.00 | 0.05 | 0.01 | 0.20 | 0.06 | 0.37 | 0.07 | 0.02 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.02 | 0.02 | 0.07 | 0.04 | 0.00 | 0.00 | 0.09 | 0.02 |
| SLC25A23 | ENSG00000125648 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.10 | 0.00 | 0.01 | 0.01 | 0.09 | 0.01 | 0.06 | 0.03 | 0.09 | 0.01 | 0.09 | 0.02 | 0.11 | 0.01 | 0.08 | 0.02 | 0.03 | 0.00 | 0.06 | 0.00 | 0.05 | 0.01 | 0.12 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.08 | 0.11 | 0.58 | 0.03 | 0.17 | 0.01 | 0.21 | 0.02 | 0.56 | 0.17 | 0.02 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.09 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.05 | 0.04 | 0.03 |
| CTLA4 | ENSG00000163599 | 0.02 | 0.03 | 0.04 | 0.02 | 0.00 | 0.03 | 0.01 | 0.02 | 0.02 | 0.13 | 0.00 | 0.00 | 0.00 | 0.06 | 0.05 | 0.02 | 0.13 | 0.09 | 0.08 | 0.12 | 0.14 | 0.04 | 0.06 | 0.03 | 0.02 | 0.01 | 0.03 | 0.00 | 0.07 | 0.01 | 0.09 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.24 | 0.10 | 0.05 | 0.24 | 0.05 | 0.03 | 0.06 | 0.05 | 0.08 | 0.09 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.01 | 0.01 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 |
| SHH | ENSG00000164690 | 0.03 | 0.01 | 0.04 | 0.00 | 0.05 | 0.02 | 0.02 | 0.04 | 0.04 | 0.07 | 0.00 | 0.01 | 0.00 | 0.03 | 0.10 | 0.02 | 0.07 | 0.11 | 0.03 | 0.16 | 0.10 | 0.26 | 0.03 | 0.09 | 0.02 | 0.01 | 0.03 | 0.02 | 0.03 | 0.05 | 0.06 | 0.05 | 0.00 | 0.07 | 0.05 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.09 | 0.06 | 0.57 | 0.08 | 0.03 | 0.08 | 0.04 | 0.06 | 0.07 | 0.23 | 0.06 | 0.19 | 0.01 | 0.05 | 0.00 | 0.06 | 0.02 | 0.09 | 0.09 | 0.01 | 0.05 | 0.02 | 0.00 | 0.03 | 0.17 | 0.05 |
| CLUL1 | ENSG00000079101 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.01 | 0.03 | 0.09 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.02 | 0.19 | 0.04 | 0.16 | 0.03 | 0.26 | 0.06 | 0.06 | 0.02 | 0.02 | 0.01 | 0.02 | 0.05 | 0.03 | 0.03 | 0.03 | 0.02 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.04 | 0.04 | 0.15 | 0.11 | 0.06 | 0.03 | 0.05 | 0.03 | 0.10 | 0.07 | 0.17 | 0.12 | 0.00 | 0.11 | 0.00 | 0.01 | 0.03 | 0.04 | 0.02 | 0.03 | 0.01 | 0.04 | 0.00 | 0.00 | 0.04 | 0.02 |
| AQP3 | ENSG00000165272 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.08 | 0.03 | 0.00 | 0.00 | 0.01 | 0.10 | 0.08 | 0.01 | 0.35 | 0.04 | 0.14 | 0.03 | 0.21 | 0.02 | 0.14 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.02 | 0.01 | 0.24 | 0.01 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.11 | 0.08 | 0.01 | 0.01 | 0.04 | 0.01 | 0.04 | 0.05 | 0.09 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.04 | 0.07 | 0.00 | 0.00 | 0.05 | 0.04 |
| PRDM8 | ENSG00000152784 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.09 | 0.03 | 0.00 | 0.00 | 0.02 | 0.06 | 0.04 | 0.03 | 0.10 | 0.04 | 0.04 | 0.03 | 0.04 | 0.06 | 0.02 | 0.05 | 0.01 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.02 | 0.09 | 0.05 | 0.03 | 0.08 | 0.02 | 0.02 | 0.02 | 0.00 | 0.00 | 0.06 | 0.03 | 0.10 | 0.19 | 0.03 | 0.03 | 0.02 | 0.02 | 0.15 | 0.07 | 0.07 | 0.05 | 0.03 | 0.02 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.03 |
| ERAP2 | ENSG00000164308 | 0.06 | 0.01 | 0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.17 | 0.02 | 0.09 | 0.00 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.02 | 0.08 | 0.00 | 0.07 | 0.03 | 0.09 | 0.01 | 0.12 | 0.00 | 0.12 | 0.01 | 0.02 | 0.00 | 0.05 | 0.03 | 0.04 | 0.00 | 0.02 | 0.12 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.07 | 0.06 | 0.48 | 0.00 | 0.05 | 0.03 | 0.06 | 0.05 | 0.16 | 0.05 | 0.04 | 0.01 | 0.00 | 0.00 | 0.07 | 0.04 | 0.00 | 0.01 | 0.02 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.03 |
| GRIA3 | ENSG00000125675 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.06 | 0.04 | 0.04 | 0.01 | 0.03 | 0.01 | 0.08 | 0.02 | 0.08 | 0.02 | 0.08 | 0.01 | 0.11 | 0.02 | 0.09 | 0.03 | 0.03 | 0.01 | 0.04 | 0.02 | 0.01 | 0.00 | 0.08 | 0.03 | 0.00 | 0.01 | 0.06 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.04 | 0.02 | 0.20 | 0.04 | 0.06 | 0.02 | 0.02 | 0.03 | 0.05 | 0.26 | 0.07 | 0.11 | 0.00 | 0.02 | 0.00 | 0.00 | 0.10 | 0.02 | 0.01 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 |
| MAST2 | ENSG00000086015 | 0.00 | 0.02 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.04 | 0.11 | 0.03 | 0.00 | 0.00 | 0.09 | 0.03 | 0.09 | 0.03 | 0.08 | 0.02 | 0.06 | 0.02 | 0.04 | 0.02 | 0.03 | 0.03 | 0.02 | 0.02 | 0.02 | 0.02 | 0.01 | 0.01 | 0.03 | 0.08 | 0.00 | 0.23 | 0.03 | 0.03 | 0.01 | 0.11 | 0.00 | 0.00 | 0.06 | 0.05 | 0.39 | 0.06 | 0.08 | 0.01 | 0.08 | 0.01 | 0.17 | 0.03 | 0.11 | 0.04 | 0.06 | 0.03 | 0.02 | 0.00 | 0.04 | 0.03 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.06 | 0.02 |
| MAT1A | ENSG00000151224 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.01 | 0.08 | 0.08 | 0.04 | 0.00 | 0.00 | 0.01 | 0.03 | 0.02 | 0.02 | 0.08 | 0.05 | 0.04 | 0.04 | 0.05 | 0.04 | 0.13 | 0.04 | 0.05 | 0.02 | 0.13 | 0.03 | 0.06 | 0.00 | 0.02 | 0.04 | 0.25 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.14 | 0.04 | 0.26 | 0.15 | 0.02 | 0.02 | 0.11 | 0.05 | 0.48 | 0.03 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 |
| TNFSF14 | ENSG00000125735 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.08 | 0.00 | 0.01 | 0.01 | 0.07 | 0.01 | 0.06 | 0.04 | 0.09 | 0.02 | 0.09 | 0.02 | 0.11 | 0.00 | 0.08 | 0.03 | 0.03 | 0.01 | 0.06 | 0.00 | 0.05 | 0.01 | 0.11 | 0.00 | 0.01 | 0.01 | 0.04 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.08 | 0.13 | 0.54 | 0.03 | 0.17 | 0.02 | 0.21 | 0.02 | 0.56 | 0.21 | 0.02 | 0.02 | 0.00 | 0.04 | 0.00 | 0.00 | 0.11 | 0.01 | 0.01 | 0.02 | 0.01 | 0.00 | 0.05 | 0.05 | 0.03 |
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