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 |
| SLC25A44 | ENSG00000160785 | 0.03 | 0.00 | 0.01 | 0.00 | 0.00 | 0.03 | 0.02 | 0.03 | 0.34 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.32 | 0.00 | 0.24 | 0.00 | 0.05 | 0.01 | 0.23 | 0.00 | 0.14 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.33 | 0.00 | 0.48 | 0.01 | 0.09 | 0.03 | 0.06 | 0.00 | 0.00 | 0.00 | 0.28 | 0.01 | 0.54 | 0.02 | 0.16 | 0.00 | 0.29 | 0.00 | 0.85 | 0.01 | 0.32 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.16 | 0.01 |
| CCR5 | ENSG00000160791 | 0.00 | 0.18 | 0.00 | 0.02 | 0.08 | 0.00 | 0.00 | 0.03 | 0.07 | 0.10 | 0.00 | 0.04 | 0.00 | 0.52 | 0.01 | 0.06 | 0.01 | 0.08 | 0.00 | 0.05 | 0.01 | 0.07 | 0.01 | 0.09 | 0.00 | 0.04 | 0.03 | 0.06 | 0.00 | 0.04 | 0.03 | 0.04 | 0.00 | 0.24 | 0.01 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.07 | 0.18 | 0.01 | 0.05 | 0.02 | 0.05 | 0.03 | 0.18 | 0.05 | 0.13 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.05 | 0.00 | 0.04 | 0.00 | 0.03 | 0.02 | 0.05 |
| PTH1R | ENSG00000160801 | 0.00 | 0.18 | 0.00 | 0.02 | 0.08 | 0.00 | 0.00 | 0.03 | 0.05 | 0.10 | 0.00 | 0.04 | 0.00 | 0.56 | 0.01 | 0.06 | 0.00 | 0.09 | 0.00 | 0.06 | 0.01 | 0.08 | 0.02 | 0.11 | 0.00 | 0.05 | 0.03 | 0.06 | 0.00 | 0.05 | 0.03 | 0.04 | 0.00 | 0.24 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.15 | 0.09 | 0.19 | 0.01 | 0.05 | 0.03 | 0.05 | 0.04 | 0.25 | 0.04 | 0.11 | 0.01 | 0.04 | 0.00 | 0.01 | 0.00 | 0.10 | 0.00 | 0.06 | 0.00 | 0.04 | 0.00 | 0.03 | 0.01 | 0.05 |
| FCRL3 | ENSG00000160856 | 0.03 | 0.00 | 0.01 | 0.01 | 0.00 | 0.03 | 0.02 | 0.06 | 0.38 | 0.01 | 0.02 | 0.00 | 0.11 | 0.00 | 0.27 | 0.00 | 0.24 | 0.01 | 0.07 | 0.00 | 0.25 | 0.00 | 0.12 | 0.00 | 0.03 | 0.00 | 0.11 | 0.00 | 0.07 | 0.00 | 0.30 | 0.00 | 0.41 | 0.01 | 0.05 | 0.02 | 0.04 | 0.00 | 0.00 | 0.00 | 0.27 | 0.01 | 0.39 | 0.02 | 0.16 | 0.00 | 0.15 | 0.00 | 0.37 | 0.00 | 0.37 | 0.01 | 0.10 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.01 | 0.00 | 0.05 | 0.00 | 0.00 | 0.03 | 0.17 | 0.01 |
| CYP3A7 | ENSG00000160870 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.02 | 0.08 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.12 | 0.02 | 0.24 | 0.01 | 0.24 | 0.00 | 0.52 | 0.02 | 0.31 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.11 | 0.01 | 0.09 | 0.01 | 0.11 | 0.03 | 0.10 | 0.03 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.03 | 0.20 | 0.05 | 0.07 | 0.01 | 0.06 | 0.02 | 0.12 | 0.04 | 0.08 | 0.04 | 0.09 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 |
| CYP11B1 | ENSG00000160882 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.04 | 0.02 | 0.20 | 0.02 | 0.02 | 0.00 | 0.10 | 0.04 | 0.26 | 0.01 | 0.36 | 0.02 | 0.29 | 0.00 | 0.41 | 0.02 | 0.21 | 0.02 | 0.15 | 0.03 | 0.24 | 0.03 | 0.15 | 0.02 | 0.34 | 0.02 | 0.25 | 0.01 | 0.08 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.42 | 0.05 | 1.46 | 0.05 | 0.21 | 0.01 | 0.10 | 0.02 | 0.14 | 0.03 | 0.20 | 0.06 | 0.05 | 0.03 | 0.02 | 0.00 | 0.26 | 0.01 | 0.17 | 0.04 | 0.03 | 0.03 | 0.50 | 0.00 | 0.24 | 0.02 |
| LY6K | ENSG00000160886 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.04 | 0.02 | 0.20 | 0.02 | 0.02 | 0.00 | 0.10 | 0.04 | 0.26 | 0.01 | 0.36 | 0.02 | 0.29 | 0.00 | 0.41 | 0.02 | 0.22 | 0.02 | 0.15 | 0.03 | 0.24 | 0.03 | 0.15 | 0.01 | 0.35 | 0.02 | 0.25 | 0.01 | 0.04 | 0.00 | 0.01 | 0.03 | 0.00 | 0.01 | 0.43 | 0.05 | 1.46 | 0.05 | 0.21 | 0.01 | 0.11 | 0.02 | 0.14 | 0.03 | 0.21 | 0.06 | 0.05 | 0.03 | 0.02 | 0.00 | 0.26 | 0.01 | 0.17 | 0.03 | 0.04 | 0.03 | 0.50 | 0.00 | 0.24 | 0.02 |
| MUM1 | ENSG00000160953 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.03 | 0.02 | 0.15 | 0.05 | 0.00 | 0.03 | 0.10 | 0.02 | 0.08 | 0.03 | 0.15 | 0.01 | 0.15 | 0.02 | 0.17 | 0.03 | 0.08 | 0.01 | 0.07 | 0.02 | 0.09 | 0.00 | 0.07 | 0.04 | 0.14 | 0.04 | 0.03 | 0.22 | 0.01 | 0.01 | 0.00 | 0.00 | 0.01 | 0.01 | 0.18 | 0.03 | 0.93 | 0.04 | 0.24 | 0.01 | 0.26 | 0.02 | 0.72 | 0.22 | 0.20 | 0.00 | 0.00 | 0.00 | 0.02 | 0.07 | 0.03 | 0.04 | 0.02 | 0.08 | 0.01 | 0.04 | 0.02 | 0.05 | 0.08 |
| COL26A1 | ENSG00000160963 | 0.02 | 0.00 | 0.05 | 0.00 | 0.06 | 0.00 | 0.04 | 0.03 | 0.06 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.01 | 0.20 | 0.02 | 0.20 | 0.01 | 0.48 | 0.03 | 0.17 | 0.02 | 0.02 | 0.01 | 0.01 | 0.00 | 0.06 | 0.02 | 0.05 | 0.02 | 0.11 | 0.01 | 0.08 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.05 | 0.04 | 0.22 | 0.05 | 0.05 | 0.03 | 0.05 | 0.02 | 0.11 | 0.03 | 0.07 | 0.04 | 0.07 | 0.01 | 0.00 | 0.00 | 0.13 | 0.00 | 0.06 | 0.00 | 0.04 | 0.01 | 0.00 | 0.00 | 0.06 | 0.03 |
| PGLYRP2 | ENSG00000161031 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.06 | 0.00 | 0.01 | 0.02 | 0.12 | 0.02 | 0.07 | 0.01 | 0.25 | 0.01 | 0.07 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.01 | 0.00 | 0.13 | 0.03 | 0.00 | 0.03 | 0.35 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.81 | 0.04 | 0.01 | 0.01 | 0.25 | 0.01 | 0.36 | 0.05 | 0.17 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 |
| SCGB3A1 | ENSG00000161055 | 0.33 | 0.01 | 0.06 | 0.01 | 0.00 | 0.04 | 0.03 | 0.01 | 0.02 | 0.10 | 0.00 | 0.01 | 0.03 | 0.05 | 0.09 | 0.03 | 0.04 | 0.05 | 0.03 | 0.06 | 0.16 | 0.02 | 0.03 | 0.04 | 0.03 | 0.01 | 0.04 | 0.03 | 0.03 | 0.01 | 0.14 | 0.05 | 0.05 | 0.01 | 0.37 | 0.03 | 0.01 | 0.03 | 0.01 | 0.00 | 0.10 | 0.05 | 0.23 | 0.14 | 0.04 | 0.04 | 0.07 | 0.03 | 0.15 | 0.02 | 0.20 | 0.09 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.01 | 0.06 | 0.04 | 0.04 | 0.04 | 0.02 | 0.09 | 0.08 |
| DMKN | ENSG00000161249 | 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 | 0.01 | 0.11 | 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 | 0.63 | 0.05 | 0.22 | 0.01 | 0.18 | 0.02 | 1.50 | 0.01 | 0.29 | 0.05 | 0.01 | 0.02 | 0.00 | 0.01 | 0.08 | 0.00 | 0.02 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.05 | 0.01 |
| GRIN2C | ENSG00000161509 | 0.02 | 0.00 | 0.05 | 0.00 | 0.02 | 0.00 | 0.03 | 0.03 | 0.21 | 0.00 | 0.00 | 0.01 | 0.09 | 0.02 | 0.17 | 0.01 | 0.23 | 0.01 | 0.08 | 0.03 | 0.21 | 0.06 | 0.12 | 0.03 | 0.03 | 0.01 | 0.04 | 0.02 | 0.05 | 0.09 | 0.25 | 0.00 | 0.08 | 0.01 | 0.09 | 0.02 | 0.02 | 0.00 | 0.00 | 0.00 | 0.36 | 0.03 | 0.32 | 0.03 | 0.21 | 0.02 | 0.14 | 0.01 | 0.47 | 0.02 | 0.24 | 0.03 | 0.03 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.06 | 0.01 | 0.14 | 0.01 | 0.24 | 0.01 |
| KLHL10 | ENSG00000161594 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.01 | 0.04 | 0.05 | 0.02 | 0.01 | 0.61 | 0.02 | 0.44 | 0.03 | 0.06 | 0.00 | 0.03 | 0.02 | 0.03 | 0.03 | 0.02 | 0.03 | 0.02 | 0.01 | 0.01 | 0.16 | 0.00 | 0.11 | 0.00 | 0.00 | 0.09 | 0.09 | 0.04 | 0.15 | 0.04 | 0.05 | 0.04 | 0.06 | 0.19 | 0.09 | 0.04 | 0.12 | 0.01 | 0.01 | 0.00 | 0.02 | 0.04 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.03 |
| HCRT | ENSG00000161610 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.05 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.06 | 0.01 | 0.03 | 0.05 | 0.03 | 0.01 | 0.19 | 0.04 | 0.13 | 0.03 | 0.05 | 0.01 | 0.04 | 0.02 | 0.03 | 0.03 | 0.02 | 0.04 | 0.02 | 0.01 | 0.02 | 0.14 | 0.00 | 0.12 | 0.00 | 0.00 | 0.05 | 0.10 | 0.01 | 0.15 | 0.05 | 0.04 | 0.03 | 0.07 | 0.00 | 0.20 | 0.05 | 0.10 | 0.01 | 0.01 | 0.00 | 0.02 | 0.06 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.00 | 0.05 | 0.01 | 0.03 |
| DCD | ENSG00000161634 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.09 | 0.02 | 0.00 | 0.00 | 0.02 | 0.04 | 0.07 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.05 | 0.03 | 0.06 | 0.02 | 0.02 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.02 | 0.01 | 0.17 | 0.01 | 0.30 | 0.00 | 0.06 | 0.00 | 0.00 | 0.00 | 0.04 | 0.05 | 0.16 | 0.04 | 0.06 | 0.00 | 0.04 | 0.01 | 0.14 | 0.09 | 0.14 | 0.08 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.04 | 0.03 | 0.05 | 0.08 | 0.00 | 0.03 | 0.05 |
| SIGLEC11 | ENSG00000161640 | 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 | 0.04 | 0.32 | 0.05 | 0.07 | 0.04 | 0.06 | 0.11 | 0.15 | 0.03 | 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 |
| CD300LG | ENSG00000161649 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.15 | 0.04 | 0.02 | 0.01 | 0.01 | 0.02 | 0.04 | 0.07 | 0.01 | 0.04 | 0.06 | 0.02 | 0.02 | 0.11 | 0.01 | 0.10 | 0.02 | 0.03 | 0.01 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.03 | 0.02 | 0.01 | 0.07 | 0.14 | 0.00 | 0.09 | 0.00 | 0.00 | 0.04 | 0.10 | 0.03 | 0.14 | 0.04 | 0.03 | 0.03 | 0.07 | 0.12 | 0.19 | 0.05 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.00 | 0.05 | 0.01 | 0.05 |
| PLCD3 | ENSG00000161714 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.04 | 0.02 | 0.01 | 0.00 | 0.03 | 0.00 | 0.05 | 0.01 | 0.06 | 0.04 | 0.01 | 0.01 | 0.14 | 0.02 | 0.07 | 0.02 | 0.02 | 0.00 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.02 | 0.02 | 0.01 | 0.07 | 0.08 | 0.00 | 0.07 | 0.00 | 0.00 | 0.03 | 0.11 | 0.03 | 0.11 | 0.07 | 0.03 | 0.04 | 0.07 | 0.05 | 0.18 | 0.04 | 0.08 | 0.01 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.05 | 0.01 | 0.05 |
| AQP5 | ENSG00000161798 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.06 | 0.03 | 0.00 | 0.00 | 0.00 | 0.04 | 0.06 | 0.02 | 0.03 | 0.02 | 0.01 | 0.03 | 0.06 | 0.03 | 0.05 | 0.04 | 0.02 | 0.00 | 0.02 | 0.01 | 0.01 | 0.05 | 0.01 | 0.01 | 0.00 | 0.01 | 0.19 | 0.00 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 | 0.10 | 0.06 | 0.03 | 0.01 | 0.05 | 0.01 | 0.33 | 0.06 | 0.05 | 0.09 | 0.02 | 0.00 | 0.00 | 0.01 | 0.10 | 0.03 | 0.00 | 0.04 | 0.02 | 0.05 | 0.00 | 0.00 | 0.06 | 0.05 |
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