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 |
| PLCG1 | ENSG00000124181 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.09 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.02 | 0.04 | 0.09 | 0.01 | 0.01 | 0.02 | 0.03 | 0.01 | 0.09 | 0.01 | 0.08 | 0.01 | 0.13 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.00 | 0.04 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.03 | 0.05 | 0.10 | 0.02 | 0.02 | 0.05 | 0.01 | 0.20 | 0.04 | 0.17 | 0.03 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.02 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 |
| MORC3 | ENSG00000159256 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.03 | 0.09 | 0.03 | 0.00 | 0.00 | 0.00 | 0.01 | 0.01 | 0.03 | 0.02 | 0.04 | 0.02 | 0.03 | 0.04 | 0.06 | 0.04 | 0.04 | 0.02 | 0.01 | 0.04 | 0.05 | 0.01 | 0.01 | 0.02 | 0.00 | 0.05 | 0.03 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 | 0.12 | 0.08 | 0.12 | 0.01 | 0.03 | 0.01 | 0.04 | 0.03 | 0.04 | 0.07 | 0.03 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 |
| CROT | ENSG00000005469 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.05 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.04 | 0.02 | 0.20 | 0.02 | 0.17 | 0.01 | 0.40 | 0.01 | 0.22 | 0.01 | 0.03 | 0.01 | 0.01 | 0.00 | 0.08 | 0.00 | 0.08 | 0.02 | 0.04 | 0.01 | 0.03 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.19 | 0.05 | 0.07 | 0.02 | 0.02 | 0.02 | 0.09 | 0.03 | 0.07 | 0.05 | 0.13 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.02 | 0.00 | 0.06 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 |
| HDAC5 | ENSG00000108840 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.17 | 0.04 | 0.03 | 0.01 | 0.00 | 0.02 | 0.00 | 0.07 | 0.01 | 0.04 | 0.05 | 0.02 | 0.01 | 0.12 | 0.02 | 0.08 | 0.03 | 0.02 | 0.01 | 0.03 | 0.03 | 0.05 | 0.01 | 0.04 | 0.03 | 0.08 | 0.01 | 0.07 | 0.14 | 0.00 | 0.10 | 0.00 | 0.00 | 0.03 | 0.10 | 0.02 | 0.13 | 0.02 | 0.03 | 0.05 | 0.07 | 0.09 | 0.19 | 0.06 | 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 | 0.06 |
| ASXL1 | ENSG00000171456 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.01 | 0.29 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.08 | 0.02 | 0.22 | 0.00 | 0.17 | 0.00 | 0.06 | 0.00 | 0.06 | 0.01 | 0.14 | 0.00 | 0.23 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.05 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.02 | 0.26 | 0.02 | 0.20 | 0.00 | 0.17 | 0.01 | 1.18 | 0.00 | 0.10 | 0.02 | 0.06 | 0.00 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 |
| PTAR1 | ENSG00000188647 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.03 | 0.05 | 0.00 | 0.01 | 0.03 | 0.03 | 0.01 | 0.05 | 0.06 | 0.06 | 0.01 | 0.03 | 0.08 | 0.03 | 0.04 | 0.05 | 0.01 | 0.01 | 0.02 | 0.02 | 0.00 | 0.00 | 0.02 | 0.03 | 0.00 | 0.15 | 0.05 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.05 | 0.05 | 0.10 | 0.15 | 0.01 | 0.03 | 0.02 | 0.03 | 0.07 | 0.11 | 0.16 | 0.02 | 0.02 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.04 | 0.00 | 0.00 | 0.03 | 0.03 |
| NR2C2 | ENSG00000177463 | 0.00 | 0.18 | 0.00 | 0.01 | 0.07 | 0.00 | 0.01 | 0.02 | 0.32 | 0.01 | 0.02 | 0.03 | 0.01 | 0.03 | 0.03 | 0.04 | 0.02 | 0.04 | 0.02 | 0.02 | 0.04 | 0.03 | 0.07 | 0.05 | 0.01 | 0.03 | 0.03 | 0.07 | 0.01 | 0.02 | 0.06 | 0.01 | 0.00 | 0.18 | 0.07 | 0.01 | 0.01 | 0.04 | 0.00 | 0.00 | 0.16 | 0.02 | 0.15 | 0.20 | 0.01 | 0.02 | 0.05 | 0.04 | 0.08 | 0.11 | 0.24 | 0.02 | 0.05 | 0.05 | 0.00 | 0.00 | 0.00 | 0.05 | 0.03 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.03 | 0.06 |
| PHF23 | ENSG00000040633 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.23 | 0.05 | 0.03 | 0.00 | 0.01 | 0.00 | 0.02 | 0.01 | 0.05 | 0.01 | 0.02 | 0.02 | 0.03 | 0.03 | 0.04 | 0.02 | 0.02 | 0.00 | 0.03 | 0.00 | 0.04 | 0.02 | 0.03 | 0.00 | 0.15 | 0.01 | 0.08 | 0.02 | 0.05 | 0.00 | 0.04 | 0.00 | 0.00 | 0.01 | 0.07 | 0.13 | 0.04 | 0.00 | 0.03 | 0.05 | 0.02 | 0.09 | 0.18 | 0.06 | 0.36 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.01 | 0.00 | 0.07 | 0.00 | 0.00 | 0.01 | 0.04 |
| SLC25A13 | ENSG00000004864 | 0.01 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.06 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.08 | 0.01 | 0.22 | 0.01 | 0.23 | 0.01 | 0.62 | 0.02 | 0.32 | 0.01 | 0.03 | 0.01 | 0.01 | 0.01 | 0.07 | 0.01 | 0.12 | 0.02 | 0.18 | 0.01 | 0.10 | 0.03 | 0.01 | 0.02 | 0.00 | 0.00 | 0.07 | 0.03 | 0.17 | 0.06 | 0.05 | 0.01 | 0.07 | 0.02 | 0.26 | 0.03 | 0.11 | 0.04 | 0.11 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.04 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.06 | 0.02 |
| IL10RB | ENSG00000243646 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.01 | 0.02 | 0.02 | 0.04 | 0.03 | 0.04 | 0.02 | 0.03 | 0.00 | 0.06 | 0.01 | 0.02 | 0.02 | 0.00 | 0.02 | 0.03 | 0.00 | 0.02 | 0.01 | 0.05 | 0.03 | 0.15 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.11 | 0.04 | 0.02 | 0.01 | 0.03 | 0.00 | 0.04 | 0.03 | 0.08 | 0.04 | 0.02 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.02 | 0.02 | 0.02 | 0.02 | 0.03 | 0.00 | 0.01 | 0.01 |
| PVRL3 | ENSG00000177707 | 0.00 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.02 | 0.04 | 0.04 | 0.02 | 0.00 | 0.02 | 0.00 | 0.02 | 0.04 | 0.02 | 0.15 | 0.03 | 0.05 | 0.01 | 0.09 | 0.02 | 0.06 | 0.02 | 0.00 | 0.01 | 0.01 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.10 | 0.02 | 0.00 | 0.05 | 0.00 | 0.00 | 0.05 | 0.02 | 0.35 | 0.04 | 0.04 | 0.01 | 0.03 | 0.01 | 0.14 | 0.08 | 0.11 | 0.06 | 0.01 | 0.01 | 0.00 | 0.01 | 0.02 | 0.00 | 0.01 | 0.04 | 0.00 | 0.05 | 0.00 | 0.00 | 0.02 | 0.06 |
| CYP19A1 | ENSG00000137869 | 0.00 | 0.00 | 0.00 | 0.01 | 0.14 | 0.01 | 0.01 | 0.04 | 0.05 | 0.03 | 0.00 | 0.00 | 0.07 | 0.15 | 0.01 | 0.04 | 0.04 | 0.06 | 0.04 | 0.03 | 0.03 | 0.03 | 0.01 | 0.06 | 0.01 | 0.03 | 0.00 | 0.05 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.01 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.08 | 0.08 | 0.19 | 0.01 | 0.10 | 0.00 | 0.07 | 0.08 | 0.26 | 0.11 | 0.04 | 0.02 | 0.03 | 0.00 | 0.00 | 0.06 | 0.05 | 0.00 | 0.02 | 0.00 | 0.08 | 0.00 | 0.00 | 0.04 | 0.10 |
| ADRA1D | ENSG00000171873 | 0.01 | 0.00 | 0.01 | 0.00 | 0.03 | 0.00 | 0.01 | 0.03 | 0.03 | 0.03 | 0.00 | 0.00 | 0.00 | 0.03 | 0.03 | 0.04 | 0.12 | 0.01 | 0.03 | 0.03 | 0.06 | 0.03 | 0.05 | 0.01 | 0.06 | 0.04 | 0.05 | 0.08 | 0.00 | 0.03 | 0.04 | 0.01 | 0.00 | 0.03 | 0.05 | 0.08 | 0.00 | 0.01 | 0.00 | 0.00 | 0.06 | 0.05 | 0.28 | 0.07 | 0.05 | 0.01 | 0.09 | 0.02 | 0.09 | 0.06 | 0.07 | 0.09 | 0.00 | 0.02 | 0.00 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.00 | 0.03 | 0.02 |
| CNP | ENSG00000173786 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.06 | 0.02 | 0.00 | 0.00 | 0.01 | 0.02 | 0.05 | 0.01 | 0.03 | 0.05 | 0.02 | 0.01 | 0.35 | 0.03 | 0.17 | 0.03 | 0.06 | 0.01 | 0.04 | 0.02 | 0.03 | 0.03 | 0.04 | 0.03 | 0.02 | 0.01 | 0.04 | 0.16 | 0.01 | 0.12 | 0.00 | 0.00 | 0.06 | 0.10 | 0.03 | 0.15 | 0.03 | 0.04 | 0.04 | 0.07 | 0.02 | 0.14 | 0.05 | 0.11 | 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 |
| KLHL7 | ENSG00000122550 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 0.01 | 0.10 | 0.01 | 0.00 | 0.00 | 0.03 | 0.00 | 0.13 | 0.01 | 0.15 | 0.01 | 0.05 | 0.01 | 0.20 | 0.01 | 0.08 | 0.01 | 0.05 | 0.00 | 0.03 | 0.00 | 0.02 | 0.00 | 0.06 | 0.00 | 0.00 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.02 | 0.19 | 0.19 | 0.05 | 0.00 | 0.09 | 0.03 | 0.45 | 0.01 | 0.19 | 0.04 | 0.06 | 0.00 | 0.00 | 0.01 | 0.09 | 0.05 | 0.00 | 0.00 | 0.05 | 0.01 | 0.00 | 0.00 | 0.09 | 0.02 |
| PA2G4 | ENSG00000170515 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.01 | 0.08 | 0.02 | 0.00 | 0.00 | 0.02 | 0.02 | 0.11 | 0.01 | 0.04 | 0.02 | 0.01 | 0.02 | 0.12 | 0.03 | 0.19 | 0.01 | 0.02 | 0.00 | 0.02 | 0.01 | 0.02 | 0.01 | 0.06 | 0.00 | 0.05 | 0.01 | 0.10 | 0.01 | 0.06 | 0.00 | 0.00 | 0.00 | 0.05 | 0.05 | 0.30 | 0.04 | 0.04 | 0.00 | 0.21 | 0.00 | 0.56 | 0.07 | 0.16 | 0.07 | 0.01 | 0.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.01 | 0.03 | 0.06 | 0.05 | 0.00 | 0.00 | 0.05 | 0.03 |
| CDK14 | ENSG00000058091 | 0.01 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.06 | 0.02 | 0.00 | 0.00 | 0.03 | 0.02 | 0.07 | 0.01 | 0.25 | 0.02 | 0.18 | 0.01 | 0.61 | 0.02 | 0.38 | 0.03 | 0.03 | 0.01 | 0.02 | 0.00 | 0.12 | 0.01 | 0.12 | 0.03 | 0.18 | 0.01 | 0.11 | 0.01 | 0.00 | 0.02 | 0.00 | 0.00 | 0.07 | 0.02 | 0.17 | 0.09 | 0.07 | 0.01 | 0.04 | 0.02 | 0.11 | 0.03 | 0.13 | 0.05 | 0.13 | 0.00 | 0.00 | 0.01 | 0.13 | 0.00 | 0.02 | 0.00 | 0.07 | 0.01 | 0.00 | 0.00 | 0.04 | 0.03 |
| NPEPL1 | ENSG00000215440 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.06 | 0.03 | 0.00 | 0.00 | 0.03 | 0.02 | 0.28 | 0.01 | 0.04 | 0.04 | 0.01 | 0.01 | 0.10 | 0.01 | 0.23 | 0.00 | 0.14 | 0.00 | 0.08 | 0.00 | 0.05 | 0.00 | 0.10 | 0.00 | 0.00 | 0.01 | 0.05 | 0.02 | 0.01 | 0.00 | 0.00 | 0.00 | 0.37 | 0.02 | 0.38 | 0.05 | 0.03 | 0.03 | 0.10 | 0.01 | 0.17 | 0.00 | 0.25 | 0.04 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.02 | 0.02 | 0.00 | 0.00 | 0.09 | 0.01 |
| BTN3A2 | ENSG00000186470 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.02 | 0.21 | 0.03 | 0.00 | 0.01 | 0.02 | 0.05 | 0.08 | 0.01 | 0.07 | 0.06 | 0.02 | 0.04 | 0.11 | 0.10 | 0.06 | 0.05 | 0.03 | 0.02 | 0.04 | 0.03 | 0.02 | 0.04 | 0.10 | 0.01 | 0.06 | 0.08 | 0.04 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.03 | 0.35 | 0.05 | 0.09 | 0.03 | 0.04 | 0.01 | 0.20 | 0.02 | 0.03 | 0.06 | 0.01 | 0.01 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.01 | 0.01 | 0.00 | 0.11 | 0.00 | 0.13 | 0.01 |
| AHCYL1 | ENSG00000168710 | 0.00 | 0.01 | 0.00 | 0.01 | 0.00 | 0.00 | 0.01 | 0.05 | 0.05 | 0.06 | 0.00 | 0.00 | 0.00 | 0.33 | 0.02 | 0.13 | 0.02 | 0.14 | 0.00 | 0.12 | 0.05 | 0.12 | 0.03 | 0.07 | 0.00 | 0.06 | 0.00 | 0.07 | 0.00 | 0.02 | 0.02 | 0.03 | 0.00 | 0.11 | 0.06 | 0.04 | 0.00 | 0.26 | 0.00 | 0.00 | 0.04 | 0.10 | 0.16 | 0.14 | 0.01 | 0.08 | 0.03 | 0.03 | 0.08 | 0.06 | 0.08 | 0.10 | 0.03 | 0.04 | 0.00 | 0.00 | 0.00 | 0.05 | 0.01 | 0.01 | 0.03 | 0.02 | 0.00 | 0.03 | 0.08 | 0.10 |
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