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 |
| ATP1B1 | ENSG00000143153 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.05 | 0.46 | 0.01 | 0.02 | 0.02 | 0.10 | 0.04 | 0.15 | 0.01 | 0.25 | 0.01 | 0.04 | 0.01 | 0.27 | 0.01 | 0.14 | 0.00 | 0.04 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.23 | 0.00 | 0.30 | 0.01 | 0.00 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.21 | 0.02 | 0.32 | 0.02 | 0.16 | 0.01 | 0.10 | 0.00 | 0.29 | 0.00 | 0.41 | 0.05 | 0.09 | 0.00 | 0.00 | 0.00 | 0.47 | 0.00 | 0.01 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.16 | 0.01 |
| CREG1 | ENSG00000143162 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.06 | 0.49 | 0.01 | 0.02 | 0.02 | 0.10 | 0.03 | 0.15 | 0.01 | 0.24 | 0.01 | 0.05 | 0.01 | 0.22 | 0.00 | 0.11 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.05 | 0.00 | 0.27 | 0.00 | 0.30 | 0.01 | 0.02 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.21 | 0.01 | 0.33 | 0.02 | 0.15 | 0.00 | 0.11 | 0.01 | 0.27 | 0.00 | 0.41 | 0.03 | 0.09 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.15 | 0.01 |
| GPA33 | ENSG00000143167 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.06 | 0.54 | 0.01 | 0.02 | 0.00 | 0.10 | 0.03 | 0.15 | 0.01 | 0.25 | 0.01 | 0.05 | 0.01 | 0.21 | 0.00 | 0.11 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.06 | 0.00 | 0.26 | 0.00 | 0.30 | 0.01 | 0.04 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.23 | 0.01 | 0.34 | 0.02 | 0.13 | 0.00 | 0.12 | 0.01 | 0.28 | 0.00 | 0.43 | 0.03 | 0.09 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.14 | 0.01 |
| XCL1 | ENSG00000143184 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.48 | 0.01 | 0.02 | 0.02 | 0.10 | 0.03 | 0.14 | 0.01 | 0.25 | 0.01 | 0.04 | 0.00 | 0.20 | 0.01 | 0.13 | 0.00 | 0.03 | 0.00 | 0.08 | 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 | 0.34 | 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 |
| XCL2 | ENSG00000143185 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.48 | 0.01 | 0.02 | 0.00 | 0.10 | 0.03 | 0.14 | 0.01 | 0.24 | 0.01 | 0.03 | 0.01 | 0.20 | 0.01 | 0.13 | 0.00 | 0.03 | 0.00 | 0.08 | 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 |
| MGST3 | ENSG00000143198 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.06 | 0.61 | 0.01 | 0.02 | 0.00 | 0.10 | 0.02 | 0.19 | 0.00 | 0.26 | 0.01 | 0.05 | 0.01 | 0.21 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.08 | 0.00 | 0.06 | 0.00 | 0.26 | 0.00 | 0.30 | 0.01 | 0.05 | 0.04 | 0.04 | 0.00 | 0.00 | 0.00 | 0.24 | 0.01 | 0.36 | 0.02 | 0.16 | 0.00 | 0.13 | 0.01 | 0.31 | 0.00 | 0.32 | 0.03 | 0.09 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.14 | 0.01 |
| NR1I3 | ENSG00000143257 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.05 | 0.95 | 0.00 | 0.02 | 0.00 | 0.10 | 0.01 | 0.26 | 0.00 | 0.27 | 0.00 | 0.06 | 0.00 | 0.33 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.14 | 0.00 | 0.06 | 0.00 | 0.33 | 0.00 | 0.30 | 0.01 | 0.16 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.33 | 0.00 | 0.36 | 0.02 | 0.18 | 0.00 | 0.16 | 0.00 | 0.41 | 0.00 | 0.39 | 0.03 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.17 | 0.01 |
| FCRL5 | ENSG00000143297 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.07 | 0.36 | 0.02 | 0.02 | 0.00 | 0.11 | 0.00 | 0.28 | 0.00 | 0.24 | 0.00 | 0.07 | 0.00 | 0.25 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.32 | 0.00 | 0.41 | 0.01 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.26 | 0.01 | 0.39 | 0.02 | 0.15 | 0.00 | 0.14 | 0.00 | 0.37 | 0.00 | 0.44 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.17 | 0.01 |
| CRABP2 | ENSG00000143320 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.04 | 0.32 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.29 | 0.00 | 0.23 | 0.00 | 0.04 | 0.01 | 0.24 | 0.00 | 0.13 | 0.00 | 0.04 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.32 | 0.00 | 0.43 | 0.01 | 0.09 | 0.02 | 0.06 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.43 | 0.02 | 0.16 | 0.00 | 0.18 | 0.00 | 0.47 | 0.01 | 0.35 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| HDGF | ENSG00000143321 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.01 | 0.04 | 0.32 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.28 | 0.00 | 0.23 | 0.01 | 0.04 | 0.01 | 0.24 | 0.01 | 0.13 | 0.00 | 0.04 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.33 | 0.00 | 0.43 | 0.01 | 0.09 | 0.02 | 0.07 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.43 | 0.02 | 0.16 | 0.00 | 0.18 | 0.00 | 0.50 | 0.01 | 0.35 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.05 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| ECM1 | ENSG00000143369 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.57 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.44 | 0.00 | 0.30 | 0.00 | 0.09 | 0.01 | 0.24 | 0.00 | 0.23 | 0.00 | 0.03 | 0.00 | 0.18 | 0.00 | 0.06 | 0.00 | 0.39 | 0.00 | 0.43 | 0.01 | 0.22 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.44 | 0.01 | 0.75 | 0.02 | 0.20 | 0.00 | 0.33 | 0.00 | 0.62 | 0.00 | 0.45 | 0.02 | 0.14 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.22 | 0.01 |
| ADAMTSL4 | ENSG00000143382 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.64 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.44 | 0.00 | 0.30 | 0.00 | 0.09 | 0.01 | 0.24 | 0.00 | 0.24 | 0.00 | 0.03 | 0.00 | 0.18 | 0.00 | 0.06 | 0.00 | 0.40 | 0.00 | 0.43 | 0.01 | 0.23 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.45 | 0.00 | 0.77 | 0.02 | 0.22 | 0.00 | 0.34 | 0.00 | 0.54 | 0.00 | 0.45 | 0.02 | 0.14 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.22 | 0.01 |
| CTSK | ENSG00000143387 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.65 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.45 | 0.01 | 0.30 | 0.00 | 0.08 | 0.01 | 0.24 | 0.00 | 0.24 | 0.00 | 0.03 | 0.00 | 0.17 | 0.00 | 0.06 | 0.00 | 0.40 | 0.01 | 0.43 | 0.01 | 0.23 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.42 | 0.00 | 0.76 | 0.02 | 0.21 | 0.00 | 0.33 | 0.00 | 0.54 | 0.00 | 0.47 | 0.02 | 0.13 | 0.00 | 0.00 | 0.00 | 0.28 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.00 | 0.21 | 0.01 |
| DYRK3 | ENSG00000143479 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.07 | 0.06 | 0.01 | 0.00 | 0.07 | 0.01 | 0.13 | 0.01 | 0.09 | 0.01 | 0.06 | 0.00 | 0.17 | 0.06 | 0.06 | 0.01 | 0.04 | 0.00 | 0.12 | 0.02 | 0.00 | 0.00 | 0.19 | 0.01 | 0.18 | 0.02 | 0.01 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.21 | 0.11 | 0.07 | 0.00 | 0.07 | 0.02 | 0.24 | 0.04 | 0.03 | 0.18 | 0.03 | 0.02 | 0.01 | 0.00 | 0.18 | 0.10 | 0.00 | 0.01 | 0.04 | 0.02 | 0.09 | 0.00 | 0.15 | 0.02 |
| TAF1A | ENSG00000143498 | 0.01 | 0.02 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.07 | 0.10 | 0.05 | 0.02 | 0.00 | 0.05 | 0.01 | 0.10 | 0.01 | 0.11 | 0.01 | 0.05 | 0.01 | 0.20 | 0.03 | 0.09 | 0.01 | 0.02 | 0.01 | 0.08 | 0.02 | 0.01 | 0.01 | 0.12 | 0.03 | 0.18 | 0.02 | 0.04 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.23 | 0.02 | 0.31 | 0.09 | 0.06 | 0.01 | 0.08 | 0.03 | 0.16 | 0.00 | 0.03 | 0.22 | 0.02 | 0.04 | 0.01 | 0.00 | 0.03 | 0.12 | 0.00 | 0.03 | 0.02 | 0.07 | 0.09 | 0.00 | 0.11 | 0.04 |
| S100A8 | ENSG00000143546 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.48 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.38 | 0.00 | 0.27 | 0.00 | 0.05 | 0.01 | 0.26 | 0.01 | 0.18 | 0.00 | 0.02 | 0.00 | 0.17 | 0.00 | 0.06 | 0.00 | 0.35 | 0.00 | 0.49 | 0.01 | 0.14 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.33 | 0.00 | 0.56 | 0.02 | 0.20 | 0.00 | 0.20 | 0.00 | 0.61 | 0.00 | 0.47 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.20 | 0.04 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.21 | 0.00 |
| SLC27A3 | ENSG00000143554 | 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 | 0.37 | 0.00 | 0.27 | 0.00 | 0.05 | 0.01 | 0.25 | 0.01 | 0.19 | 0.00 | 0.02 | 0.00 | 0.15 | 0.00 | 0.06 | 0.00 | 0.37 | 0.00 | 0.49 | 0.01 | 0.25 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.31 | 0.00 | 0.56 | 0.02 | 0.19 | 0.00 | 0.22 | 0.00 | 0.42 | 0.00 | 0.44 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.25 | 0.04 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.20 | 0.00 |
| S100A7 | ENSG00000143556 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.05 | 0.00 | 0.46 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.39 | 0.00 | 0.27 | 0.00 | 0.05 | 0.01 | 0.26 | 0.01 | 0.18 | 0.00 | 0.02 | 0.00 | 0.17 | 0.00 | 0.06 | 0.00 | 0.35 | 0.00 | 0.49 | 0.01 | 0.14 | 0.02 | 0.10 | 0.00 | 0.00 | 0.00 | 0.33 | 0.00 | 0.56 | 0.02 | 0.20 | 0.00 | 0.21 | 0.00 | 0.63 | 0.00 | 0.43 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.20 | 0.04 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.21 | 0.00 |
| SLC39A1 | ENSG00000143570 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.00 | 0.07 | 0.00 | 0.40 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.37 | 0.00 | 0.27 | 0.00 | 0.05 | 0.01 | 0.22 | 0.00 | 0.19 | 0.00 | 0.02 | 0.00 | 0.15 | 0.00 | 0.06 | 0.00 | 0.36 | 0.00 | 0.53 | 0.01 | 0.21 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.31 | 0.00 | 0.53 | 0.02 | 0.19 | 0.00 | 0.19 | 0.00 | 0.53 | 0.00 | 0.43 | 0.01 | 0.12 | 0.00 | 0.00 | 0.00 | 0.25 | 0.06 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.21 | 0.00 |
| AQP10 | ENSG00000143595 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.39 | 0.01 | 0.02 | 0.00 | 0.11 | 0.02 | 0.38 | 0.00 | 0.26 | 0.00 | 0.05 | 0.00 | 0.21 | 0.00 | 0.17 | 0.01 | 0.03 | 0.00 | 0.11 | 0.00 | 0.06 | 0.00 | 0.36 | 0.00 | 0.53 | 0.01 | 0.21 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 | 0.31 | 0.00 | 0.50 | 0.02 | 0.19 | 0.00 | 0.19 | 0.00 | 0.44 | 0.00 | 0.40 | 0.01 | 0.11 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.02 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.22 | 0.00 |
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